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- 10:53, 17 June 2020 diff hist +459 CHECKSPMUTATE current
- 20:26, 11 June 2020 diff hist +182 CHECKSPMUTATE →Potential Uses
- 14:54, 4 June 2020 diff hist +66 Pathway Gap Filling Post-CHECKSPMUTATE current
- 10:33, 4 June 2020 diff hist -1 Pathway Gap Filling Post-CHECKSPMUTATE →A Few Notes
- 10:30, 4 June 2020 diff hist +8 Pathway Gap Filling Post-CHECKSPMUTATE →Execution
- 10:29, 4 June 2020 diff hist +12 Pathway Gap Filling Post-CHECKSPMUTATE →Files Required
- 10:25, 4 June 2020 diff hist +7 Pathway Gap Filling Post-CHECKSPMUTATE →Files Required
- 10:24, 4 June 2020 diff hist +1 Pathway Gap Filling Post-CHECKSPMUTATE →Execution
- 10:24, 4 June 2020 diff hist +3 Pathway Gap Filling Post-CHECKSPMUTATE →Execution
- 10:23, 4 June 2020 diff hist +6 Pathway Gap Filling Post-CHECKSPMUTATE →Files Required
- 10:21, 4 June 2020 diff hist +6 Pathway Gap Filling Post-CHECKSPMUTATE →Note on readts
- 10:21, 4 June 2020 diff hist +7 Pathway Gap Filling Post-CHECKSPMUTATE →Files Required
- 10:19, 4 June 2020 diff hist +6 Pathway Gap Filling Post-CHECKSPMUTATE →Note on checkts
- 10:19, 4 June 2020 diff hist +95 Pathway Gap Filling Post-CHECKSPMUTATE →Execution
- 10:17, 4 June 2020 diff hist +7 Pathway Gap Filling Post-CHECKSPMUTATE →checkmin/checkts
- 10:15, 4 June 2020 diff hist +1 Pathway Gap Filling Post-CHECKSPMUTATE →Rationale
- 10:14, 4 June 2020 diff hist +3 Pathway Gap Filling Post-CHECKSPMUTATE →Introduction
- 10:10, 4 June 2020 diff hist -1 CHECKSPMUTATE →pathdata and odata.checksp files
- 10:09, 4 June 2020 diff hist -42 CHECKSPMUTATE →Making auxiliary files
- 10:04, 4 June 2020 diff hist -4 CHECKSPMUTATE →Preparation
- 10:03, 4 June 2020 diff hist +201 CHECKSPMUTATE →Potential Uses
- 10:00, 4 June 2020 diff hist +88 CHECKSPMUTATE →Preparation
- 09:57, 4 June 2020 diff hist +1 CHECKSPMUTATE
- 18:18, 3 June 2020 diff hist -2 Pathway Gap Filling Post-CHECKSPMUTATE →Cleanining Up the Pathway
- 18:18, 3 June 2020 diff hist -1 Pathway Gap Filling Post-CHECKSPMUTATE →readmin/readts
- 18:17, 3 June 2020 diff hist +794 Pathway Gap Filling Post-CHECKSPMUTATE
- 18:11, 3 June 2020 diff hist +1,620 Pathway Gap Filling Post-CHECKSPMUTATE
- 18:02, 3 June 2020 diff hist +675 Pathway Gap Filling Post-CHECKSPMUTATE →relevant_connected
- 17:56, 3 June 2020 diff hist +1,341 Pathway Gap Filling Post-CHECKSPMUTATE →relevant_connected
- 17:43, 3 June 2020 diff hist +3,690 Pathway Gap Filling Post-CHECKSPMUTATE →relevant_connected
- 17:17, 3 June 2020 diff hist +880 Pathway Gap Filling Post-CHECKSPMUTATE →now_use_connectfile_to_fill_gaps
- 17:07, 3 June 2020 diff hist +2,927 Pathway Gap Filling Post-CHECKSPMUTATE →now_use_connectfile_to_fill_gaps
- 16:43, 3 June 2020 diff hist +2,083 Pathway Gap Filling Post-CHECKSPMUTATE
- 16:26, 3 June 2020 diff hist +1,681 Pathway Gap Filling Post-CHECKSPMUTATE →all_opt_TSs
- 16:16, 3 June 2020 diff hist +2,262 Pathway Gap Filling Post-CHECKSPMUTATE →all_opt_TSs
- 16:05, 3 June 2020 diff hist +92 Pathway Gap Filling Post-CHECKSPMUTATE
- 16:02, 3 June 2020 diff hist +648 Pathway Gap Filling Post-CHECKSPMUTATE →Readmin/Readts
- 15:56, 3 June 2020 diff hist +250 Pathway Gap Filling Post-CHECKSPMUTATE →Readmin/Readts
- 15:54, 3 June 2020 diff hist -1 Pathway Gap Filling Post-CHECKSPMUTATE →Files Required
- 15:53, 3 June 2020 diff hist +891 Pathway Gap Filling Post-CHECKSPMUTATE →Readmin/Readts
- 15:49, 3 June 2020 diff hist +761 Pathway Gap Filling Post-CHECKSPMUTATE →Readmin/Readts
- 15:43, 3 June 2020 diff hist +21 Pathway Gap Filling Post-CHECKSPMUTATE →Checkmin/Checkts
- 15:42, 3 June 2020 diff hist +120 Pathway Gap Filling Post-CHECKSPMUTATE →Readmin/Readts
- 15:40, 3 June 2020 diff hist +354 Pathway Gap Filling Post-CHECKSPMUTATE →Checkmin/Checkts
- 15:38, 3 June 2020 diff hist +391 Pathway Gap Filling Post-CHECKSPMUTATE →Checkmin/Checkts
- 15:34, 3 June 2020 diff hist 0 File:Mind Map directories for group wiki.png Adk44 uploaded a new version of File:Mind Map directories for group wiki.png current
- 15:30, 3 June 2020 diff hist +504 Pathway Gap Filling Post-CHECKSPMUTATE →Checkmin/Checkts
- 15:24, 3 June 2020 diff hist -244 Pathway Gap Filling Post-CHECKSPMUTATE →Checkmin/Checkts
- 15:23, 3 June 2020 diff hist +3,054 Pathway Gap Filling Post-CHECKSPMUTATE
- 12:10, 3 June 2020 diff hist +195 Pathway Gap Filling Post-CHECKSPMUTATE →Method
- 12:08, 3 June 2020 diff hist +1 Pathway Gap Filling Post-CHECKSPMUTATE →Method
- 12:08, 3 June 2020 diff hist +62 Pathway Gap Filling Post-CHECKSPMUTATE →Method
- 12:07, 3 June 2020 diff hist 0 N File:Mind Map directories for group wiki.png
- 12:02, 3 June 2020 diff hist +305 Pathway Gap Filling Post-CHECKSPMUTATE
- 11:21, 3 June 2020 diff hist +987 N Pathway Gap Filling Post-CHECKSPMUTATE Created page with "== Introduction == This is a recommended procedure to be used following the use of CHECKSPMUTATE, if it was a pathway which was being reoptimised. CHECKSPMUTATE muta..."
- 11:12, 3 June 2020 diff hist +86 Comprehensive Contents Page →AMBER
- 11:11, 3 June 2020 diff hist +86 Comprehensive Contents Page →PATHSAMPLE
- 11:10, 3 June 2020 diff hist +107 CHECKSPMUTATE
- 17:21, 2 June 2020 diff hist +124 Comprehensive Contents Page →AMBER
- 17:18, 2 June 2020 diff hist 0 CHECKSPMUTATE →Before and After Mutation
- 17:18, 2 June 2020 diff hist +43 CHECKSPMUTATE →Before and After Mutation
- 17:16, 2 June 2020 diff hist -3 CHECKSPMUTATE →Before and After Mutation
- 17:15, 2 June 2020 diff hist -79 CHECKSPMUTATE
- 17:12, 2 June 2020 diff hist +86 CHECKSPMUTATE
- 17:08, 2 June 2020 diff hist 0 CHECKSPMUTATE
- 17:07, 2 June 2020 diff hist 0 N File:F101A Hems wiki.png current
- 17:07, 2 June 2020 diff hist 0 N File:Wt HemS wiki.png current
- 17:05, 2 June 2020 diff hist +257 CHECKSPMUTATE →pathdata and odata.checksp files
- 16:46, 2 June 2020 diff hist -2 CHECKSPMUTATE →Making auxiliary files
- 16:46, 2 June 2020 diff hist +2,257 CHECKSPMUTATE
- 16:28, 2 June 2020 diff hist +542 CHECKSPMUTATE
- 16:25, 2 June 2020 diff hist +1,574 CHECKSPMUTATE →Example of Transformation to a Homologue
- 16:17, 2 June 2020 diff hist +1 CHECKSPMUTATE →Making auxiliary file
- 16:17, 2 June 2020 diff hist 0 CHECKSPMUTATE →Making auxiliary file
- 16:16, 2 June 2020 diff hist +2 CHECKSPMUTATE →Making auxiliary file
- 16:15, 2 June 2020 diff hist +310 CHECKSPMUTATE →Making auxiliary file
- 16:12, 2 June 2020 diff hist +120 CHECKSPMUTATE →Making auxiliary file
- 16:10, 2 June 2020 diff hist +60 CHECKSPMUTATE →Making auxiliary file
- 16:07, 2 June 2020 diff hist +240 CHECKSPMUTATE →Making auxiliary file
- 16:05, 2 June 2020 diff hist +30 CHECKSPMUTATE →Making auxiliary file
- 16:04, 2 June 2020 diff hist +180 CHECKSPMUTATE →Making auxiliary file
- 16:03, 2 June 2020 diff hist +240 CHECKSPMUTATE →Making auxiliary file
- 16:00, 2 June 2020 diff hist +90 CHECKSPMUTATE →Making auxiliary file
- 15:59, 2 June 2020 diff hist +240 CHECKSPMUTATE →Making auxiliary file
- 15:57, 2 June 2020 diff hist +210 CHECKSPMUTATE →Making auxiliary file
- 15:55, 2 June 2020 diff hist +150 CHECKSPMUTATE →Making auxiliary file
- 15:53, 2 June 2020 diff hist +420 CHECKSPMUTATE →Making auxiliary file
- 15:49, 2 June 2020 diff hist +210 CHECKSPMUTATE →Making auxiliary file
- 15:47, 2 June 2020 diff hist +120 CHECKSPMUTATE →Making auxiliary file
- 15:45, 2 June 2020 diff hist +240 CHECKSPMUTATE →Making auxiliary file
- 15:43, 2 June 2020 diff hist +30 CHECKSPMUTATE →Making auxiliary file
- 15:42, 2 June 2020 diff hist +240 CHECKSPMUTATE →Making auxiliary file
- 15:39, 2 June 2020 diff hist +210 CHECKSPMUTATE →Making auxiliary file
- 15:36, 2 June 2020 diff hist +240 CHECKSPMUTATE →Making auxiliary file
- 15:34, 2 June 2020 diff hist +120 CHECKSPMUTATE →Making auxiliary file
- 15:33, 2 June 2020 diff hist +90 CHECKSPMUTATE →Making auxiliary file
- 15:31, 2 June 2020 diff hist -120 CHECKSPMUTATE →Making auxiliary file
- 15:29, 2 June 2020 diff hist -16 CHECKSPMUTATE →Making auxiliary file
- 15:29, 2 June 2020 diff hist +2 CHECKSPMUTATE →Making auxiliary file
- 15:28, 2 June 2020 diff hist +2 CHECKSPMUTATE →Making auxiliary file
- 15:26, 2 June 2020 diff hist +15 CHECKSPMUTATE →wt ChuS + haem + NADH
- 15:26, 2 June 2020 diff hist +15 CHECKSPMUTATE →Making auxiliary file
- 15:20, 2 June 2020 diff hist +131 CHECKSPMUTATE →Making auxiliary file
- 15:18, 2 June 2020 diff hist +4 CHECKSPMUTATE →Example of Transformation to a Homologue
- 15:17, 2 June 2020 diff hist +20 CHECKSPMUTATE →Making auxiliary file
- 15:16, 2 June 2020 diff hist -15 CHECKSPMUTATE →Making auxiliary file
- 15:15, 2 June 2020 diff hist +2,929 CHECKSPMUTATE
- 15:04, 2 June 2020 diff hist +433 CHECKSPMUTATE
- 15:03, 2 June 2020 diff hist +484 CHECKSPMUTATE
- 14:59, 2 June 2020 diff hist +1,440 CHECKSPMUTATE
- 14:47, 2 June 2020 diff hist +946 CHECKSPMUTATE
- 14:41, 2 June 2020 diff hist +93 CHECKSPMUTATE
- 14:39, 2 June 2020 diff hist +392 CHECKSPMUTATE
- 14:32, 2 June 2020 diff hist +2,650 CHECKSPMUTATE
- 12:14, 2 June 2020 diff hist +112 CHECKSPMUTATE
- 12:11, 2 June 2020 diff hist +296 CHECKSPMUTATE →Purpose
- 12:08, 2 June 2020 diff hist +732 CHECKSPMUTATE →Purpose
- 12:01, 2 June 2020 diff hist +1,598 N CHECKSPMUTATE Created page with "== Purpose == It can take an awfully long time to create a large database or to fully optimise a specific feature of it such as afully connected pathway showing complex prote..."
- 11:44, 2 June 2020 diff hist +124 Comprehensive Contents Page →PATHSAMPLE
- 14:20, 18 July 2019 diff hist +27 Comprehensive Contents Page →OPTIM
- 09:51, 25 June 2019 diff hist -21 Main Page
- 19:50, 4 June 2019 diff hist 0 m Comprehensive Contents Page Removed protection from "Comprehensive Contents Page"
- 19:50, 4 June 2019 diff hist 0 m Comprehensive Contents Page Protected "Comprehensive Contents Page" ([Edit=Allow only autoconfirmed users] (indefinite) [Move=Allow only autoconfirmed users] (indefinite))
- 14:16, 3 June 2019 diff hist -18 Main Page →Group Members Only
- 14:16, 3 June 2019 diff hist -131 Main Page →Group Members Only
- 13:31, 3 June 2019 diff hist 0 N File:Ray7.png current
- 13:30, 3 June 2019 diff hist 0 N File:Ray6.png current
- 13:29, 3 June 2019 diff hist 0 N File:Ray5.png current
- 13:29, 3 June 2019 diff hist 0 N File:Ray4.png current
- 13:28, 3 June 2019 diff hist 0 N File:Ray3.png current
- 11:49, 3 June 2019 diff hist 0 N File:UNTRAPexample.png current
- 11:43, 3 June 2019 diff hist 0 N File:Nendhessflu1merDSYEVR.png current
- 11:28, 3 June 2019 diff hist 0 N File:CUDAGMINspeedups.png current
- 11:27, 3 June 2019 diff hist 0 N File:2INEligandnumbering.png current
- 11:27, 3 June 2019 diff hist 0 N File:ARrbtop nolines.png current
- 11:26, 3 June 2019 diff hist 0 N File:ARprerbtop nolines.png current
- 11:26, 3 June 2019 diff hist 0 N File:Aldosereductaseprepostmin.png current
- 11:25, 3 June 2019 diff hist 0 N File:PACantechamber.png current
- 11:25, 3 June 2019 diff hist 0 N File:PACreduceAMBER14.png current
- 11:24, 3 June 2019 diff hist 0 N File:PAC2INE.png current
- 11:21, 3 June 2019 diff hist 0 N File:Histidine.gif current
- 11:20, 3 June 2019 diff hist 0 N File:AldosereductaseCYS.png current
- 10:26, 3 June 2019 diff hist +31 Wales Group →Miscellaneous/uncategorised current
- 09:55, 3 June 2019 diff hist +27 Wales Group →Comprehensive Contents Page
- 09:55, 3 June 2019 diff hist +146 Wales Group →Comprehensive Contents Page
- 14:46, 16 May 2019 diff hist +104 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 14:44, 16 May 2019 diff hist +25 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 14:43, 16 May 2019 diff hist +1 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 14:42, 16 May 2019 diff hist +6 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 14:42, 16 May 2019 diff hist +143 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 14:39, 16 May 2019 diff hist +68 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 14:37, 16 May 2019 diff hist -1 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 14:37, 16 May 2019 diff hist -2 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 14:35, 16 May 2019 diff hist +16 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 14:34, 16 May 2019 diff hist +2 Connecting Sub-databases →Step 1: Using disconnectionDPS to determine the breakdown of sub-databases within your database
- 14:32, 16 May 2019 diff hist +8 Connecting Sub-databases →Systems for which this might be particularly useful
- 14:29, 16 May 2019 diff hist +34 Connecting Sub-databases
- 14:24, 16 May 2019 diff hist +9 Connecting Sub-databases →Summary for those who don't like screeds of writing
- 14:23, 16 May 2019 diff hist +947 Connecting Sub-databases →Summary for those who don't like screeds of writing
- 14:17, 16 May 2019 diff hist -25 Connecting Sub-databases →Step 1: Using disconnectionDPS to determine the breakdown of sub-databases within your database
- 14:16, 16 May 2019 diff hist +830 Connecting Sub-databases →Summary for those who don't like screeds of writing
- 14:08, 16 May 2019 diff hist +7 Connecting Sub-databases →Step 1: Using disconnectionDPS to determine the breakdown of sub-databases within your database
- 14:07, 16 May 2019 diff hist +76 Connecting Sub-databases →Step 1: Using disconnectionDPS to determine the breakdown of sub-databases within your database
- 14:06, 16 May 2019 diff hist +10 Connecting Sub-databases →Step 4: Merging the sub-databases
- 14:05, 16 May 2019 diff hist +615 Connecting Sub-databases →How to execute steps 2 and 3?
- 14:00, 16 May 2019 diff hist +139 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 13:58, 16 May 2019 diff hist 0 Connecting Sub-databases →How to execute steps 2 and 3?
- 13:58, 16 May 2019 diff hist +1,748 Connecting Sub-databases →Summary for those who don't like screeds of writing
- 13:45, 16 May 2019 diff hist +428 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 13:43, 16 May 2019 diff hist +1,691 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 13:38, 16 May 2019 diff hist +331 Connecting Sub-databases →Context and Motivation
- 18:56, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:56, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:56, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:55, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:55, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:54, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:54, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:54, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:53, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:52, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:52, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:51, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:51, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:50, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:50, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:49, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:49, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:49, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:48, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:47, 14 May 2019 diff hist 0 N File:Fourteenth step.png current
- 18:45, 14 May 2019 diff hist +116 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:44, 14 May 2019 diff hist 0 N File:Thirteenth step.png current
- 18:43, 14 May 2019 diff hist +116 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:42, 14 May 2019 diff hist 0 N File:Twelfth step.png current
- 18:39, 14 May 2019 diff hist +113 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:38, 14 May 2019 diff hist 0 N File:Eleventh step.png current
- 18:38, 14 May 2019 diff hist +114 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:35, 14 May 2019 diff hist 0 N File:Tenth step.png current
- 18:33, 14 May 2019 diff hist +111 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:32, 14 May 2019 diff hist 0 N File:Ninth step.png current
- 18:30, 14 May 2019 diff hist +111 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:29, 14 May 2019 diff hist 0 N File:Eighth step.png current
- 18:27, 14 May 2019 diff hist +112 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:26, 14 May 2019 diff hist 0 N File:Seventh step.png current
- 18:25, 14 May 2019 diff hist +113 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:24, 14 May 2019 diff hist 0 N File:Sixth step.png current
- 18:21, 14 May 2019 diff hist +111 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:20, 14 May 2019 diff hist 0 N File:Fifth step.png current
- 18:20, 14 May 2019 diff hist +1 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:18, 14 May 2019 diff hist +110 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:17, 14 May 2019 diff hist 0 N File:Fourth step.png current
- 18:16, 14 May 2019 diff hist +112 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:15, 14 May 2019 diff hist 0 N File:Third step.png current
- 18:11, 14 May 2019 diff hist +111 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:09, 14 May 2019 diff hist 0 N File:Second step.png current
- 18:07, 14 May 2019 diff hist +130 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:06, 14 May 2019 diff hist -5 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 18:05, 14 May 2019 diff hist 0 N File:First step.png current
- 18:05, 14 May 2019 diff hist +44 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 17:54, 14 May 2019 diff hist +180 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 17:53, 14 May 2019 diff hist +187 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 17:52, 14 May 2019 diff hist +92 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 17:51, 14 May 2019 diff hist +1 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 17:50, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 17:50, 14 May 2019 diff hist +1 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 17:49, 14 May 2019 diff hist -1 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 17:49, 14 May 2019 diff hist +742 Connecting Sub-databases
- 17:47, 14 May 2019 diff hist +1,350 Connecting Sub-databases →Step 3: Organising Calculations to Attempt
- 17:24, 14 May 2019 diff hist +100 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 17:23, 14 May 2019 diff hist -1 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 17:23, 14 May 2019 diff hist -3 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 17:23, 14 May 2019 diff hist +31 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 17:22, 14 May 2019 diff hist -12 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 17:21, 14 May 2019 diff hist +14 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 17:21, 14 May 2019 diff hist -1 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 17:19, 14 May 2019 diff hist +6 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 17:18, 14 May 2019 diff hist +3 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 17:14, 14 May 2019 diff hist +1,971 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 17:01, 14 May 2019 diff hist +59 Connecting Sub-databases
- 16:57, 14 May 2019 diff hist 0 Connecting Sub-databases →Step 2: RETAINSP and CONNECTUNC LOWESTTEST
- 16:56, 14 May 2019 diff hist +915 Connecting Sub-databases
- 16:53, 14 May 2019 diff hist +899 Connecting Sub-databases
- 16:48, 14 May 2019 diff hist +1,217 Connecting Sub-databases
- 16:43, 14 May 2019 diff hist +517 Connecting Sub-databases →Step 1: Using disconnectionDPS to determine the breakdown of sub-databases within your database
- 16:39, 14 May 2019 diff hist +218 Connecting Sub-databases
- 16:33, 14 May 2019 diff hist +18 Connecting Sub-databases
- 16:33, 14 May 2019 diff hist +83 Connecting Sub-databases →Step 1: Using disconnectionDPS to determine the breakdown of sub-databases within your database
- 16:32, 14 May 2019 diff hist +32 Connecting Sub-databases →Step 1: Using disconnectionDPS to determine the breakdown of sub-databases within your database
- 16:31, 14 May 2019 diff hist +2 Connecting Sub-databases →Step 1: Using disconnectionDPS to determine the breakdown of sub-databases within your database
- 16:30, 14 May 2019 diff hist -4 Connecting Sub-databases →Step 1: Using disconnectionDPS to determine the breakdown of sub-databases within your database
- 16:30, 14 May 2019 diff hist +181 Connecting Sub-databases
- 16:28, 14 May 2019 diff hist +4 Connecting Sub-databases
- 16:28, 14 May 2019 diff hist +103 Connecting Sub-databases
- 16:27, 14 May 2019 diff hist +2,050 N Connecting Sub-databases Created page with "== Definitions == For the purposes of this tutorial, I am defining sub-databases to be sets of connected minima and transition states within a larger database. == Context a..."
- 16:13, 14 May 2019 diff hist +31 Comprehensive Contents Page →PATHSAMPLE
- 16:09, 14 May 2019 diff hist -201 Comprehensive Contents Page →Miscellaneous
- 11:33, 14 May 2019 diff hist +1,236 PATHSAMPLE current
- 11:33, 14 May 2019 diff hist -1,236 PATHSAMPLE Blanked the page Tag: Blanking
- 11:23, 14 May 2019 diff hist +1,236 PATHSAMPLE
- 11:23, 14 May 2019 diff hist -1,236 PATHSAMPLE Blanked the page Tag: Blanking
- 10:27, 14 May 2019 diff hist -3 Main Page
- 10:26, 14 May 2019 diff hist -1 Main Page
- 10:26, 14 May 2019 diff hist +4 Main Page
- 10:05, 14 May 2019 diff hist -55 Main Page
- 10:04, 14 May 2019 diff hist +55 Main Page
- 09:58, 14 May 2019 diff hist -55 Main Page
- 09:57, 14 May 2019 diff hist +55 Main Page
- 15:37, 13 May 2019 diff hist +169 Main Page →Group Members Only
- 14:06, 13 May 2019 diff hist 0 N File:Hbond group4vs6.png current
- 14:05, 13 May 2019 diff hist 0 N File:Group compare.png current
- 14:05, 13 May 2019 diff hist 0 N File:Hbond group6.png current
- 14:04, 13 May 2019 diff hist 0 N File:Naotvside18.png current
- 14:03, 13 May 2019 diff hist 0 N File:Naotvtop18.png current
- 14:02, 13 May 2019 diff hist 0 N File:Tzwithoutgr.png current
- 14:01, 13 May 2019 diff hist 0 N File:Tzwithgr.png current
- 14:00, 13 May 2019 diff hist 0 N File:Chriscleanroom1.jpg current
- 13:58, 13 May 2019 diff hist +1,762 N Victor Ruehle Created page with "Here is a collection of wiki pages I find usefule or am working on: == General == * Mercurial * Wales Group Fortran conventions for group software == Crystal struc..." current
- 13:57, 13 May 2019 diff hist 0 N File:Km591 twz3.jpg current
- 13:56, 13 May 2019 diff hist 0 N File:Km591 twz1.png current
- 13:56, 13 May 2019 diff hist 0 N File:Km591 twz2.jpg current
- 13:54, 13 May 2019 diff hist +2,539 N User:Ab2111 Created page with "== Current projects == === Torsional movesets for biomolecules: Biased Gaussian Sampling === Favrin et. al have developed a movecass for MC simulations of biomolecules: [htt..." current
- 13:53, 13 May 2019 diff hist -2 Main Page →Comprehensive Contents Page
- 13:53, 13 May 2019 diff hist -2 Main Page →Group Members Only
- 13:52, 13 May 2019 diff hist +230 N SuSE 11.1 Created page with "== Notes on SuSE 11.1 for workstations == === compilers === * pgi - even 8.0 only supports suse 10.3 (and sles 11 which is based on opensuse 11.1) * intel * pathscale - sles..." current
- 13:52, 13 May 2019 diff hist +5,291 N SuSE 10.3 workstation image Created page with "It is time to produce a spec for the next generation of the workstation image. This is to be based on SuSE 10.3 as 11.0 is too new for compiler support. We also considered Ubu..." current
- 13:51, 13 May 2019 diff hist +2,396 N SuSE 10.2 workstation image Created page with "The SuSE 10.1 workstation image is rolled out and working; it's time to start worrying about 10.2 == Improvements in 10.2 == * LDAP support: your password will be your L..." current
- 13:50, 13 May 2019 diff hist +3,466 N SuSE 10.1 workstation image Created page with "We need a new workstation image as SuSE 9.3 won't be supported for very much longer (ends Easter 2007). In order that I don't have to do this this again in six months I'm goin..." current
- 13:50, 13 May 2019 diff hist +1,451 N Upgrading sword Created page with "This happened, so I leave this page here only for reference. Sword needs an upgrade. I'd like to move it to SuSE 9.3. The destiny upgrade went OK, whic..." current
- 13:50, 13 May 2019 diff hist +898 N Upgrading destiny Created page with "Destiny is to be upgraded to SuSE and at the same time have a new disk installed to give a bigger /scratch and /usr/local. I will be withdrawing CRYSTAL98 and Portland versio..." current
- 13:49, 13 May 2019 diff hist +4,126 N Blacklisting Compilers Created page with "Some compiler versions just don't work with our code. This might be due to a bug in the compiler, or maybe the compiler version is too old and doesn't include the features we..." current
- 13:49, 13 May 2019 diff hist +7,696 N Compiler Flags Created page with "This page serves as documentation for the mysterious compiler flags: please keep it up to date. It includes a description of what each flag does and a list of flags in use for..." current
- 13:48, 13 May 2019 diff hist -29 Comprehensive Contents Page →Miscellaneous/uncategorised
- 13:48, 13 May 2019 diff hist -1,512 Comprehensive Contents Page →Group practice
- 13:46, 13 May 2019 diff hist +2,417 N Uploading non image files to the wiki Created page with "For security reasons, the 'Upload file' functionality of the wiki only lets you upload images with .png, .gif, .jpg and .jpeg extensions. This can be a bit of a pain when you..." current
- 13:46, 13 May 2019 diff hist +2,086 N Printing files from the command line using 'lpr' Created page with "You cannot print files directly from one of the clusters so the first thing you need to do is transfer the file to your workstation. This can be done using the ''scp'' command..." current
- 13:46, 13 May 2019 diff hist +436 N Finding bugs in latex documents that will not compile Created page with "When you try to compile a latex document that contains an error - the compilation will halt with an (often cryptic) error message and a '''?''' prompt. At this point, you can..." current
- 13:45, 13 May 2019 diff hist +77 N Running programs in the background Created page with "To run a job in the background, type & after your command, i.e. [command] &" current
- 13:45, 13 May 2019 diff hist +320 N Installing packages on your managed CUC3 workstation Created page with "Although we don't have access to apt-get, or the package management application in Ubuntu, it appears you are able to access the 'aptitude' package manager still using sudo: <..." current
- 13:44, 13 May 2019 diff hist +5,661 N A guide to using SLURM to run GPU jobs on pat Created page with "We now have a queueing system set up for use with some of our GPU machines. The head node is pat.ch.private.cam.ac.uk and all jobs should be submitted to the queue from there...." current
- 13:44, 13 May 2019 diff hist +2,209 N A guide to using SLURM to run PATHSAMPLE Created page with "Below are two example submission scripts for running PATHSAMPLE jobs on clusters using the SLURM queueing system, e.g. volkhan and sinister. Keyword SLURM can be used to launc..." current
- 13:43, 13 May 2019 diff hist +1,164 N Identifying job on a node Created page with "Sometimes it may happen that on some node you have more than one job running and only one among them you need to kill. How find which one it is? If you only know which output..." current
- 13:43, 13 May 2019 diff hist +4,493 N Submitting jobs, interactively or to a cluster queue system Created page with "This is a brief summary for those who haven't found/read the [http://www-co.ch.cam.ac.uk/facilities/compute-servers/theory/maui/maui-pbs-introduction.html documentation] provi..." current
- 13:42, 13 May 2019 diff hist +1,222 N Removing an excessive number of files from a directory - when 'rm' just isn't enough Created page with "If you have say 10000 files, all named ''output.[number]'', trying to get rid of them all with the usual ''rm output.*'' command won't work as when you expand the * to produce..." current
- 13:42, 13 May 2019 diff hist +1,157 N Conversion between different image file formats Created page with "The ''convert'' command is an extremely powerful way of changing an image into a different format, or modifying it in ways you never thought possible! It is only available on..." current
- 13:42, 13 May 2019 diff hist +1,056 N Conversion between different data file formats Created page with "==== For AMBER ==== xyz -> inpcrd awk '{printf("%12.7f %11.7f %11.7f "), $1, $2, $3} {getline} {printf("%11.7f %11.7f %11.7f\n"), $1, $2, $3}' input.xyz > input.inpcr..." current
- 13:41, 13 May 2019 diff hist +162 N Using tar and gzip to compress/uncompress files Created page with "Compress with bzip2 directory temp tar cvfj temp.tar.bz temp Uncompress with bzip2 directory temp tar xvfj temp.tar.bz Cat compressed file bzcat temp.bz" current
- 13:40, 13 May 2019 diff hist +1,244 N Sorting a file by multiple columns Created page with "If you have a file you want to sort using multiple columns of numbers, the ''sort'' command is your new best friend! For example, here is a section from a file I'm trying to..." current
- 13:40, 13 May 2019 diff hist +10,094 N Short 'awk' examples Created page with "The examples below were prepared by Eric Pement and taken from this [http://www.student.northpark.edu/pemente/awk/awk1line.txt web page]. As the ''awk'' syntax is so....random..." current
- 13:39, 13 May 2019 diff hist +4,095 N Quick guide to awk Created page with "== Introduction == awk is useful for combining regular expressions with editing and other functions so that you can easily modify text files with conditional flow control. T..." current
- 13:39, 13 May 2019 diff hist +18,380 N Short 'sed' examples Created page with "The examples below were prepared by Eric Pement and taken from this [http://sed.sourceforge.net/sed1line.txt web page]. A detailed description can be found [http://www.gnu.org..." current
- 13:38, 13 May 2019 diff hist +1,094 N Mounting sharedscratch locally Created page with "Thanks to Phil in Computer Support for this: 1) If you're not on a computer within the theory sector, first you'll need to set up the VPN client as instructed [http://www-co...." current
- 13:38, 13 May 2019 diff hist +720 N Using 'ssh-keygen' to automatically log you into clusters from your workstation Created page with "== Using ssh-copy-id == Just run the command ssh-copy-id [user@]machine for example, to ssh and scp to clust from your workstation, just issue the command ssh-copy-id clu..." current
- 13:37, 13 May 2019 diff hist +1,341 N Transfering files to and from your workstation Created page with "First off you should only be using programs that use the ssh libraries for transferring files. Furthermore you should not be using a system that allows rcp or rlogin because t..." current
- 13:37, 13 May 2019 diff hist +1,811 N Setting up aliases to quickly log you in to a different machine Created page with "== Using ssh config == Create the file ''~/.ssh/config'' if it does not exists. Set up the config file. There are lots of guides around. Say you want to log into sinister unde..." current
- 13:36, 13 May 2019 diff hist +427 N Bash history searching Created page with "I learned these commands from looking over David's shoulder and have found them very useful. ===Search bash history=== A very useful way to quickly repeat a previous command,..." current
- 13:36, 13 May 2019 diff hist +115 N Bash loop tricks Created page with "===Simple counter loop=== <pre> for ((i=1; i <= $max ; i++)) do echo $i done </pre> $max can be a number also." current
- 13:36, 13 May 2019 diff hist +950 N Piping and redirecting output from one command or file to another Created page with "Piping entails sending standard output to the standard input of a linux command. Pipes are the primary power of using the command line. They can be used with sed, awk, perl,..." current
- 13:35, 13 May 2019 diff hist +3,796 N Basic linux commands everyone should know! Created page with "Here are a few simple linux commands that should make life a bit easier for you. Please everyone, add anything you think would be useful! You may want to read the computer of..." current
- 13:33, 13 May 2019 diff hist +831 N Zippo Sicortex machine Created page with "Please record useful notes about the new SiCortex machine here. == Specifying nodes == A node specific hello world program: <pre> $ cat hosthello.c #include <unistd.h> #inc..." current
- 13:32, 13 May 2019 diff hist +6,504 N Tardis scheduling policy Created page with "We appear to need to take another look at tardis's scheduling policy. Greg and Catherine would like everyone to agree on a policy and then give it a reasonable trial before st..." current
- 13:32, 13 May 2019 diff hist +313 N See unpacked nodes Created page with "To do this, type: diagnose -n | grep 'Running' | awk '{print $1, $3}' I'm curious as to why this is useful, can you explain? --Catherine 13:41, 27 August 2..." current
- 13:31, 13 May 2019 diff hist +3,763 N Remastering Knoppix Created page with "Quick notes on how I made a remastered Knoppix for David Wales. Closely based on an article by Robert Bernier at linuxdevcenter.com but updated for a newer Knoppix. This ass..." current
- 13:31, 13 May 2019 diff hist +1,135 N Rama upgrade Created page with "Rama needs upgrading to a supported operating system. SLES10 looks like a good choice as it will last for the rest of the machine's natural life. Things that will change: *..." current
- 13:30, 13 May 2019 diff hist +3,179 N Proposed changes to backup and archiving Created page with "==Current systems== We need more backup space as workstation disks are getting larger and we have acquired several more clusters. We currently have about 3Tb split over t..." current
- 13:30, 13 May 2019 diff hist +2,197 N Porfuncs Documentation Created page with "Various system functions are included in the porfuncs module, generated from porfuncs.sh. They are documented here as a reference for developers. Please use these subroutines,..." current
- 13:29, 13 May 2019 diff hist +392 N Other IT stuff Created page with "Made this page so I can provide links to older IT pages and not clutter up the 'headlines' on the front page. * New mek-quake * Backup strategy * Proposed changes..." current
- 13:29, 13 May 2019 diff hist +2,756 N Optimization tricks Created page with "== Profiling == * Compile your code with pgf90 and the following flags: FFLAGS= -Mextend -g -traceback -pg * Run GMIN on your input. Note that gmon.out is produced. * Run..." current
- 13:28, 13 May 2019 diff hist +4,577 N NECI Parallelization Created page with "It seems that there are two main aims of NECI Parallelization * To Reduce Integral Cache storage needs (and also to therefore compute the stored integrals in parallel) * To Su..." current
- 13:28, 13 May 2019 diff hist +1,532 N Migrating to the new SVN server Created page with "All of these steps assume you put the repository in ~/svn so modify as needed! * update your local copy (important! If this doesn't work, it means the old server has been tak..." current
- 13:28, 13 May 2019 diff hist +3,996 N Mercurial Created page with "== General introduction == Mercurial is what you call a distributed version management system. That means, you have a local copy of the repository (including the full history)..." current
- 13:27, 13 May 2019 diff hist +891 N Torque and Maui Created page with "Notes on local use of Torque and Maui. Probably not much in here for end users, unless you're very curious. == Environment passing == Weirdism: qsub -v PATH does not work o..." current
- 13:27, 13 May 2019 diff hist +698 N Maui compilation Created page with "It's 7/6/06 at time of writing On new mek-quake torque-2.1 does not work with current Maui because they have chnaged the libraries from libpbs.a to libtorque.a . Found a patc..." current
- 13:26, 13 May 2019 diff hist +195 N New mek-quake Created page with "This is a large cluster system to be used by the Wales and Vendruscolo groups. Differences from Clust Mek-quake initial setup notes Maui compilation Mek-qua..." current
- 13:26, 13 May 2019 diff hist +1,052 N Mek-quake initial setup notes Created page with "So far: * PBS set up with Maui (see Maui compilation) * Modules mainly there although probably a few bugs left * Prologue and epilogue working OK (and safe for concurrenc..." current
- 13:26, 13 May 2019 diff hist +3,235 N Mek-quake Queueing system Created page with "Please write your thoughts about the mek-quake queueing system here. And please sign your posts! --Catherine 16:26, 21 June 2006 (BST) My thoughts are that w..." current
- 13:25, 13 May 2019 diff hist +2,842 N Lapack compilation Created page with "I had some problems using the atlas modules, which seem to be not applicable to all machines (e.g. 64-bit P4s). I compiled my own lapack routines (available from [http://www...." current
- 13:25, 13 May 2019 diff hist +825 N LDAP plans Created page with "== LDAP Plans == None of this is set in stone, although it is now looking like it will actually happen. why? * authentication of users (initially so they can share passwor..." current
- 13:24, 13 May 2019 diff hist +1,225 N Intel Trace Analyzer and Collector Created page with "This is a thing that came as part of the Intel cluster toolkit on zero but I am still figuring out how to use it, sp these are rough notes. module add itac mpicc -trace -o..." current
- 13:24, 13 May 2019 diff hist +464 N Fixing thunderbird links Created page with "Under suse 10.2 on steelhorn clicking on URL's in emails ceased to open the link in firefox. To fix this you need to add the following lines to your ~/.thunderbird/<xxxxxxxx>...." current
- 13:23, 13 May 2019 diff hist -29 Comprehensive Contents Page →Miscellaneous
- 13:22, 13 May 2019 diff hist +265 N Differences from Clust Created page with "* Scheduling done by the core rather than the node, so you can run single-core jobs. * Queue names consequently different * node scratch filesystems available under /nodescrat..." current
- 13:22, 13 May 2019 diff hist +1,734 N Decoding heat capacity curves Created page with "This is a short introduction on how to analyse and decode heat capacity curve features (D.J. Wales ''Phys. Rev. E'' '''95''', 030105(R), 2017). After creating your data base..."
- 13:22, 13 May 2019 diff hist +2,756 N Computing values only once Created page with "== Profiling == * Compile your code with pgf90 and the following flags: FFLAGS= -Mextend -g -traceback -pg * Run GMIN on your input. Note that gmon.out is produced. * Run..." current
- 13:21, 13 May 2019 diff hist +346 N Computer Office services Created page with "This has moved to [http://hogthrob.ch.cam.ac.uk/mediawiki/index.php?title=Computer_Officer_Services the COs' wiki]. COs only! And even more recently, this has gone public on..." current
- 13:21, 13 May 2019 diff hist 0 N File:Chain crossing.png current
- 13:20, 13 May 2019 diff hist +124 N Chain crossing Created page with "File:chain_crossing.png Example of a path containing two chain-crossings. Coarse-grained C-alpha model with SB keyword." current
- 13:20, 13 May 2019 diff hist +3,990 N Backup strategy Created page with "Thoughts about our backup strategy. We currently back up via home grown scripts to JBODs and that works very well. We have no central fileserver and there is no political sup..." current
- 13:19, 13 May 2019 diff hist +1,659 N Parameter-scanning script Created page with "<pre> #!/bin/csh # need data.template, qsub.template and input.*.crd in the top level directory (from which this script is run) # as well as all the other necessary files fo..." current
- 13:18, 13 May 2019 diff hist +17,962 N Computing CHARMM FF energy using GMIN, MMTSB and CHARMM Created page with "Below script (compare.sh) computes the Charmm FF energy of the same structure. Useful for cross-validating force field settings in GMIN data file, CHARMM input file and MMTSB..." current
- 13:18, 13 May 2019 diff hist +587 N David's .inputrc file Created page with "This will reduce your typing. It sets up ESC then . as the last item on the previous line and ESC then , and backward search in history matching the start of what you have alr..." current
- 13:17, 13 May 2019 diff hist +1,116 N Recommended bash aliases Created page with "~wales/.bashalias Copying ~wales/.inputrc to your home directory will also reduce your typing. It sets up ESC then . as the last item on the previous line and ESC then , and..." current
- 13:17, 13 May 2019 diff hist +1,658 N Pdb to movie.py Created page with " #! /usr/bin/env python """ Calculates the movieseg or a OPTIM coord file from a given PDB file arguments: 50 format('CA: ',3(f8.3,1x),'CB: ',3(f8..." current
- 13:16, 13 May 2019 diff hist +996 N Colourdiscon.py Created page with "Script useful for DISCONNECTIVITY users To do this save the code in ''colourdiscon.py'' file, change privileges of this file: chmod 755 colourdiscon.py and type: ./Colou..." current
- 12:16, 13 May 2019 diff hist +4,201 N Local rigid body in OPTIM Created page with "Here we describe our implementation of local rigid body in OPTIM. ---- POTENTIAL ---- Currently I have only done this for CHARMM and NAB only. ---- MAKEIMAGE ---- Currently..." current
- 12:16, 13 May 2019 diff hist +3,260 N Local Rigid Body Framework Created page with "== Introduction == In this framework you can group arbitrary sets of atoms into rigid bodies. It currently works only in GMIN, but I will soon implement this in OPTIM too. You..." current
- 12:16, 13 May 2019 diff hist +20,574 N Rigid body input files for proteins using genrigid-input.py Created page with "== Overview == The use of rigid bodies requires two files: the rbodyconfig file (definition of rigid bodies) and the coordsinirigid file. The genrigid-input.py creates those f..." current
- 12:15, 13 May 2019 diff hist +1,682 N Automatic Rigid Body Grouping Created page with "== Introduction == For large systems, grouping the rigid bodies can be tedious and painful. I intend to automate this with a pdb file as an input. Unfortunately depending on f..." current
- 12:15, 13 May 2019 diff hist +3,152 N Computing normal modes in angle-axis Created page with "On this page I will describe how you can compute normal modes in angle-axis framework. It is likely that you may have to implement your own potential (until rigid body sandbox..." current
- 12:14, 13 May 2019 diff hist +1,040 N Angle-axis framework Created page with "= Introduction = In the angle-axis framework, rotations are described by a vector of rotation, while its magnitude is the angle of rotation. A good review on rotations in gene..." current
- 12:14, 13 May 2019 diff hist +5,958 N GenCoords Models Created page with "The following parametric models are defined for use with the GenCoords program. The parameters listed here are specified at run time as param1, param2, ..., paramNp in an..." current
- 12:13, 13 May 2019 diff hist +2,149 N GenCoords Created page with "GenCoords is a Fortran program to generate arbitrary arrangements of ellipsoids interacting with the paramonov-yaliraki potential. A series of user defined parametric mode..." current
- 12:13, 13 May 2019 diff hist +1,853 N Gencoords Created page with "GenCoords is a Fortran program to generate arbitrary arrangements of ellipsoids interacting with the paramonov-yaliraki potential. A series of user defined parametric mode..." current
- 12:13, 13 May 2019 diff hist +1,544 N Ellipsoid.xyz Created page with "The ellipsoid.xyz file is the output of GMIN when using the PY keyword. The file defines the positions and orientations of the set of ''repulsive'' ellipsoids for each [..." current
- 12:12, 13 May 2019 diff hist +37 N Ellipsoid.model.xyz Created page with "Same as the ellipsoid.xyz format." current
- 12:11, 13 May 2019 diff hist +899 N Ellipsoid.model Created page with "The ellipsoid.model file is used to specify the parametric model that GenCoords uses to arrange a set of ellipsoids in a starting pattern. The file has the following forma..." current
- 12:11, 13 May 2019 diff hist +2,664 N Density of states and thermodynamics from energy distributions at different temperatures Created page with "This is a tutorial for a set of MATLAB scripts which takes as input potential energy values observed for different replicas in a temperature Replica Exchange (REX) simulation..." current
- 12:10, 13 May 2019 diff hist +710 N Xmgrace Created page with "The below command will read in a saved session file, read some data in column format (blank space delimited). Use the index and the second column as the X and Y axises. A pos..." current
- 12:10, 13 May 2019 diff hist +638 N Xmakemol Created page with "A program for visualizing atomic and molecular systems. It is fast and flexible enough to view clusters, and bioploymers The input format has one atom per line with an atom i..." current
- 12:09, 13 May 2019 diff hist +2,147 N Xfig Created page with "<h2>LaTeX fonts in Xfig figures</h2> Xfig supports LaTex fonts. Fig files are thus a convenient intermediate file format when generating figures for LaTeX documents. <h3>Man..." current
- 12:09, 13 May 2019 diff hist 0 N File:VmdAnnotate.jpg current
- 12:09, 13 May 2019 diff hist +8,489 N VMD script to annotate each frame of a trajectory Created page with "'''annotateTraj.tcl''' contains procedures to annotate each frame of a pdb trajectory file with data from the pdb file (e.g. energy from the header line of each frame) or comp..." current
- 12:08, 13 May 2019 diff hist +762 N PlotGMINms.tcl Created page with "The plotGMINms function is a script to plot out ellipsoid.xyz files which are the output from GMIN when using the PY potential keyword or GenCoords when generating..." current
- 12:08, 13 May 2019 diff hist +658 N Useful .vmdrc file Created page with "VMD has some useful features, but also a number of irritating startup options. Fortunately VMD is highly configurable. Add the following in a file calle .vmdrc for improved (..." current
- 12:07, 13 May 2019 diff hist +2,706 N Path2xyz.py Created page with "Script useful for AMBER9 and NAB users ''path.info'' file can be converted to xyz format using Python program presented below. To do this save the code in ''path2xyz.py'' fi..." current
- 12:00, 13 May 2019 diff hist +1,102 N Loading coordinate files into VMD with the help of an AMBER topology file Created page with "AMBER topology files have a lot more information in them than simple .pdbs so sometimes it's really useful to be able to load them in directly, for example when you want to lo..." current
- 11:59, 13 May 2019 diff hist 0 N File:Molefacture.png current
- 11:59, 13 May 2019 diff hist +3,326 N Using VMD to display and manipulate '.pdb' files Created page with "VMD's default input format is pdb and so it isn't necessary to specify a file extension if loading from the command line, so the following syntax could be used to load several..." current
- 11:58, 13 May 2019 diff hist +1,768 N VMD Created page with "VMD is a molecular visualization program installed on all workstations and clusters. The official documentation can be found [http://www.ks.uiuc.edu/Research/vmd/current/ug/ug..."
- 11:58, 13 May 2019 diff hist +2,732 N Extractedmin2pdb.py Created page with "Program useful for AMBER9 and NAB users If you extracted minima from ''points.min'' file and you have ''extractedmin'' file you can use Python program presented below to con..." current
- 11:58, 13 May 2019 diff hist +3,511 N Path2pdb.py Created page with "Script useful for AMBER9 and NAB users ''path.info'' file can be easy converted to the PDB format using Python program presented below. PDB file can be loaded to VMD and you..." current
- 11:57, 13 May 2019 diff hist +3,310 N Advanced colouring Created page with "You can do all sorts of weird and wonderful colouring with Pymol - but the syntax is slightly cryptic. You can find some examples on the Pymol Wiki [http://www.pymolwiki.o..." current
- 11:57, 13 May 2019 diff hist 0 N File:Ray2.png current
- 11:56, 13 May 2019 diff hist 0 N File:Ray1.png current
- 11:56, 13 May 2019 diff hist +5,214 N Producing sexy ray-traced images Created page with "Pardon the title but you'll understand when you see the results! === Before you ray trace === Before you start playing with ray tracing, you need to be sure that you're happy..." current
- 11:55, 13 May 2019 diff hist +1,102 N Loading AMBER prmtop and inpcrd files into Pymol Created page with "AMBER topology files have a lot more information in them than simple .pdbs so sometimes it's really useful to be able to load them in directly, for example when you want to lo..." current
- 11:55, 13 May 2019 diff hist +1,668 N Pymol Created page with "Pymol is an open-source molecular visualisation program (binaries, full documentation are not freely available, however). Compilation of v1.1 is straightforward (v1.2 is in b..." current
- 11:54, 13 May 2019 diff hist +769 N Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays Created page with "GMIN jobs on large systems (e.g. 5000 LJ atoms) can sometimes fail with memory allocation errors like this one: 0: ALLOCATE: 18446744071814864320 bytes requested; not enoug..." current
- 11:54, 13 May 2019 diff hist +1,723 N Pgprof Created page with "Profiling an executable can give useful information on where particular calculations spend the majority of their time, so that you can go for the big win in terms of recoding..." current
- 11:53, 13 May 2019 diff hist +6,320 N Simulations using OPEP Created page with "=== Why you might want to use OPEP === OPEP is coarse grained force field providing a potential for proteins and RNA. It can speed up calculations significantly, particularly..." current
- 11:53, 13 May 2019 diff hist +1,047 N REX (Replica EXchange MD) with the MMTSB-toolset Created page with "The MMTSB Toolset is a group of perl scripts which can be used to setup and run energy minimization, structural analysis and MD (both constant temperature and replica exchange..." current
- 11:52, 13 May 2019 diff hist +676 N Installing and setting up the MMTSB toolset Created page with "The latest version (Sep 2011) of MMTSB [http://mmtsb.org] is installed in /home/ss2029/SWins/mmtsb_toolset on CLUST. To use it set the following variables in your .bashrc: <..." current
- 11:40, 13 May 2019 diff hist +1,047 N MMTSB-toolset Created page with "The MMTSB Toolset is a group of perl scripts which can be used to setup and run energy minimization, structural analysis and MD (both constant temperature and replica exchange..." current
- 11:39, 13 May 2019 diff hist +3,350 N Latex2html Created page with "The latex2html script takes a latex document, and turns it into an equivalent set of HTML pages - broken down by section and then subsection. It generates an index.html page l..." current
- 11:38, 13 May 2019 diff hist +2,614 N Installing GROMACS on Clust Created page with "* Download GMX (gromacs-4.5.4.tar.gz [http://www.gromacs.org/Downloads]) and FFTW ( fftw-3.2.2.tar.gz [http://www.fftw.org/download.html]) source codes and extract in ~/SW..." current
- 11:38, 13 May 2019 diff hist +827 N Linear and non-linear regression in gnuplot Created page with "You can fit a simple linear regression to a set of data quickly using gnuplot: <pre> # Fit a linear polynomial to the data. # These are the primary instructions for linear re..." current
- 11:37, 13 May 2019 diff hist +675 N Plotting data in real time Created page with "If your code produces output in real time during a run, it can be both informative and interesting to be able to view the results as they come in. This can be done simply usin..." current
- 11:37, 13 May 2019 diff hist +2,280 N Plotting a quick histogram in gnuplot using the raw data Created page with "You can use the below script to plot a quick and dirty histogram of your data. There are three methods here, only method 1 is uncommented. The only variables you need to set a..." current
- 11:36, 13 May 2019 diff hist +718 N Gnuplot Created page with "gnuplot is an open source graphing program. The homepage is located [http://www.gnuplot.info/ here] and has full documentation. It is often very difficult to find useful comma..." current
- 11:35, 13 May 2019 diff hist +2,786 N DMACRYS interface Created page with "== The interface == The current idea of the interface is to use the dmacrys main code (routine CASCAD) to parse the input files and initialize all variables. At the point the..." current
- 11:35, 13 May 2019 diff hist +3,371 N Constructing Free Energy Disconnectivity Graphs Created page with "This is a short summary of how you can construct a free energy disconnectivity graph from a potential energy stationary point database. '''To start off you will need the fol..." current
- 11:34, 13 May 2019 diff hist +2,569 N If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing) Created page with "Making a charmm19 .crd file from an experimental PDB structure is not so straightforward, I've found. The same can be true if the PDB file has missing atoms. Apart from charm..." current
- 11:33, 13 May 2019 diff hist +11,790 N Calculating order parameters Created page with "When constructing a potential/free energy surface, or trying to understand the landscape topology by colouring a disconnectivity graph, you need to calculate order parameters..." current
- 11:33, 13 May 2019 diff hist +3,684 N Calculating molecular properties Created page with "Top level: CHARMM This script can be used as a template to compute properties of a molecule. Here, it reads in the crd and psf file generate above for alanine dipeptide a..." current
- 11:32, 13 May 2019 diff hist +3,836 N Calculating energy of a conformation Created page with "Top level: CHARMM This script can be used as a template to compute properties of a molecule. Here, it reads in the crd and psf file generate above for alanine dipeptide a..." current
- 11:32, 13 May 2019 diff hist +2,443 N Converting between '.crd' and '.pdb' Created page with "You can actually convert between '.xyz', '.pdb' and '.crd' formats using ''awk'' and other shell commands. There is more info on the conversion between different data file f..." current
- 11:31, 13 May 2019 diff hist +14,527 N Generating pdb, crd and psf for a peptide sequence Created page with "Top level: CHARMM Below script does for CHARMM what Leap does for AMBER (see Setting_up) -- generates input files given a peptide sequence. Here, it generates struc..." current
- 11:30, 13 May 2019 diff hist +3,711 N CPMDInput Created page with "The following options for the local CPMD code are in addition to the options given in the manual for CPMD v3.11.1. Please keep any changes to this page up-to-date with the LO..." current
- 11:30, 13 May 2019 diff hist +2,455 N CamCASP/CodeExamples/DirectAccess Created page with "<pre> program directaccess !Write a direct access file and read it. !Written with the hope of tracing a bug in gfortran - if it is a bug! implicit none integer, parameter ::..." current
- 11:30, 13 May 2019 diff hist +633 N CamCASP/ToDo/Memory Created page with "CamCASP => ToDo => Memory == Memory == What are the large objects in the code and what do we do about them? # Non-DF Hessians: o^2 v^2 # TAO, TMO..." current
- 11:29, 13 May 2019 diff hist +3,785 N CamCASP/ToDo/diskIO Created page with "CamCASP => ToDo => Disk I/O == Disk I/O == We currently spend a '''lot''' of time in disk I/O. Three years ago the situation was not so bad: we us..." current
- 11:29, 13 May 2019 diff hist +493 N CamCASP/Bugs Created page with "CamCASP => Bugs ==CamCASP Bugs== 7. Incorrect behaviour of polarizabilities 6. Rotation bugs 5. CamCASP/Bugs/5|GA..." current
- 11:28, 13 May 2019 diff hist +453 N CamCASP/Notes Created page with "CamCASP => Notes ==Notes on CamCASP usage== * Rotating integrals * Energy Scans with CamCASP * CamCASP/Notes/3 | E..." current
- 11:28, 13 May 2019 diff hist +1,138 N CamCASP/Programming/5/example1 Created page with "CamCASP => Programming => Auxiliary Basis sets Example 1 Input file <pre> Title DF and integral tests: 1s1p basis..." current
- 11:27, 13 May 2019 diff hist +533 N CamCASP/Programming Created page with "CamCASP => Programming == Programmers Notes == * Status * Basis functions * CamCASP/Programming/2 | The..." current
- 10:32, 13 May 2019 diff hist +180 N CamCasp Created page with "Bugs http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/CamCasp/Bugs To Do http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/CamCasp/ToDo --ajs1 14:45, 20 October 2008..." current
- 10:32, 13 May 2019 diff hist +1,588 N Aux2bib Created page with "'''aux2bib''' is part of the bibtools package, which you can obtain [https://ctan.org/pkg/bibtools here]. As you might be able to guess from the name, it takes a .aux file fro..." current
- 10:31, 13 May 2019 diff hist +2,753 N Perm-prmtop.py Created page with "'''What is it and why is it important?''' We have noticed that the AMBER9 potential is not symmetric with respect to permutations of identical atoms e.g. hydrogen atoms in th..." current
- 10:31, 13 May 2019 diff hist +5,610 N Performing a hydrogen-bond analysis Created page with "An analysis of the hydrogen-bonding network can provide useful structural information in many situations. For example, it can be used to classify minima (and hence colour disc..." current
- 10:30, 13 May 2019 diff hist +12,903 N REMD with AMBER Created page with "===Setting up AMBER REX=== To run REMD with AMBER you need '''sander.MPI'''. You can either copy it (clust:~bs360/bin/sander.MPI) or create your own. To do so you have to cop..." current
- 10:30, 13 May 2019 diff hist +1,300 N Evaluating different components of AMBER energy function with SANDER Created page with "===Editing Evaluating different components of AMBER energy function with SANDER=== After running AMBGMIN (with 'DUMPSTRUCTURES', 'SAVE 5' set in GMIN 'data' file), it is in..." current
- 10:29, 13 May 2019 diff hist +3,196 N Running GMIN with MD move steps AMBER Created page with "Running GMIN with AMBER with MD move steps can be more efficient than with random cartesian move steps. To do so one needs the GMIN input file <b>data</b>, the AMBER file <b>m..." current
- 10:29, 13 May 2019 diff hist +442 N Producing a PDB from a coordinates and topology file Created page with "If you have AMBER installed on your workstation, or on a cluster in your home directory (so you have $AMBERHOME set in your enviroment), you can easily produce pdb files f..." current
- 10:28, 13 May 2019 diff hist +7,304 N Symmetrising AMBER topology files Created page with "== Symmetrising a Simple Protein System == === The Basics === When LEap is used to generate AMBER topology files ('''coords.prmtop''') it doesn't do a very good job of ensur..."
- 10:27, 13 May 2019 diff hist 0 N File:Tamiflu.gif current
- 10:27, 13 May 2019 diff hist +17,913 N Preparing an AMBER topology file for a protein plus ligand system Created page with "When you want to use AMBER, either on its own to run MD, or interfaced with any of the group software (GMIN, OPTIM or PATHSAMPLE), you need to have two files a..." current
- 10:26, 13 May 2019 diff hist +185 N Using Molfacture to edit molecules and add hydrogens Created page with "This is part of the AMBER topology file generation tutorial, I will write this bit last though before I forget the more important stuff! --csw34 17:09, 12 May..." current
- 10:26, 13 May 2019 diff hist +5,005 N Preparing an AMBER topology file for a protein system Created page with "When you want to use AMBER, either on its own to run MD, or interfaced with any of the group software (GMIN, OPTIM or PATHSAMPLE), you need to have two files a..."
- 10:25, 13 May 2019 diff hist +2,975 N Simple scripts for LEaP to create topology and coordinate files Created page with "To start work with AMBER you need files defining your system (topology and coordinates) and driving file with keyword defining conditions for molecular dynamics. The detai..." current
- 10:25, 13 May 2019 diff hist +5,728 N Generating parameters using RESP charges from GAMESS-US Created page with "This tutorial is for anyone wanting to generate restricted electrostatic potential (RESP) charges for a custom ligand or other molecule. The starting point is an AMBER .pr..." current
- 10:24, 13 May 2019 diff hist +396 N Generating parameters using AMBER's built in General Forcefield (gaff) Created page with "If system contains residue(s) or ligand(s) which is not parametrized in AMBER libraries and there is no force field parameters for it, you need to calculate them :) [http..." current
- 10:24, 13 May 2019 diff hist +1,737 N Using AMBER 14 on the GPU and compute clusters Created page with "===Using the pre-compiled AMBER 14 source=== We have a site license for AMBER 14, and it has been pre-compiled for you to use on the GPU and compute clusters. You can fin..." current
- 10:23, 13 May 2019 diff hist +3,188 N Notes on AMBER 12 interface Created page with "The AMBER 12 interface is based on ''pmemd'' rather than ''sander''. There are many limitations on ''pmemd'', predominantly that it lacks: * Analytical second derivatives; *..." current
- 10:23, 13 May 2019 diff hist +13 N Quasi-continuous interpolation for biomolecules Created page with "More soon ..." current
- 10:22, 13 May 2019 diff hist +17,293 N Notes on MINPERMDIST Created page with "The subroutine that must not be named. Bringing of headaches. Bane of Friday afternoons. Mother of alignment algorithms. This page aims to collect useful information on how MI..." current
- 10:21, 13 May 2019 diff hist +7,372 N Biomolecules in PATHSAMPLE Created page with "== Overview == The use of PATHSAMPLE to explore the energy landscapes of biomolecules can be tricky. This page gives an overview for the use of AMBER12 for large biological s..." current
- 10:21, 13 May 2019 diff hist +602 N When PATHSAMPLE finds a connected path, but using DIJKSTRA 0 fails to find the connected path Created page with "If your PATHSAMPLE runs has finished with a connected path found, running DIJKSTRA 0 to calculate the rates of this path can sometimes fail by outputing that there is no conne..." current
- 10:21, 13 May 2019 diff hist +520 N Path.info file is not read, causes PATHSAMPLE to die Created page with "Occasionally PATHSAMPLE will crash due to a path.info error. Chances are an OPTIM job died, so the number of min-ts-min triples are incomplete. One needs to remove the last..." current
- 10:20, 13 May 2019 diff hist +673 N If you lost file min.data, but still you have points.min Created page with "If it happens that you lost ''min.data'', but still you have ''points.min'', do not loose your heart! Go to page [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Relaxing_existi..." current
- 10:19, 13 May 2019 diff hist +522 N If things go wrong... Created page with "* Problems with memory in GT calculations: including segmentation faults with more-or-less informative messages. Try recompiling a 64-bit executable (after a make clean, of c..." current
- 10:19, 13 May 2019 diff hist +5,210 N Relaxing existing transition states with new potential and creating new database Created page with "Sometimes it may happen that you need to change potential. All transition states that you found using previous potential can be relaxed in new potential and you do not need to..." current
- 10:19, 13 May 2019 diff hist +4,970 N Relaxing existing minima with new potential and creating new database Created page with "Sometimes it may happen that you need to change potential. All minima that you found using previous potential can be relaxed in new potential and you do not need to start your..." current
- 10:18, 13 May 2019 diff hist +3,077 N Identifying the k fastest paths between endpoints using KSHORTESTPATHS Created page with "When analysing a folding mechanism from the fastest path (the path the makes the largest contribution to the steady-state rate constant), you may want to examine how common th..." current
- 10:18, 13 May 2019 diff hist +485 N Calculating rate constants (SGT, DGT, and SDGT) Created page with "== SGT - Sparse optimised graph transformation rate calculation == [http://pdfserve.informaworld.com/899789_731200496_746054025.pdf Trygubenko and D. J. Wales 06 ] == DGT..." current
- 10:17, 13 May 2019 diff hist +3,565 N Fine tuning UNTRAP Created page with "When you're optimising a path using ''SHORTCUT'' and ''SHORTCUT BARRIER'', you often add many minima to the database, some of which will not be well connected. These minima ma..." current
- 10:17, 13 May 2019 diff hist +4,070 N Using BHINTERP to find minima between two end points Created page with "'''When using AMBER''' On the beginning you need to have two optimized structures which are called endpoints. Often they are initial and final structures of studied path..." current
- 10:16, 13 May 2019 diff hist +822 N Adding a model for PATHSAMPLE Created page with "'''Under Construction''' This is rough outline of the subrounties that need to be changed to add a new model to PATHSAMPLE. Your mileage will vary a bit with respect to the d..." current
- 10:15, 13 May 2019 diff hist +460 N IMPORTANT: Using PATHSAMPLE safely on sinister Created page with "sinister does not have 'rsh' installed on the nodes. Because of this, you need to run PATHSAMPLE slightly differently on sinister. ==Use the SSH keyword== Just add 'SSH' to..." current
- 10:14, 13 May 2019 diff hist +1,019 N Dijkstra test.py Created page with "'''What is it and why is it important?''' For large distances in PATHSAMPLE it can happen that many minima are found around the provided A and B minimum, but not between them..." current
- 18:28, 10 May 2019 diff hist +875 N Thomson problem in OPTIM Created page with "This is what I have done to make the Thomson problem works in OPTIM: 1. copy Gthomson.f90 from GMIN and work out the Hessian 2. Fudge the number of atoms in fetchz.f 3. In..." current
- 18:27, 10 May 2019 diff hist +1,845 N BLJ60 example setup Created page with "In this example the objective was to link a crystal structure to a minimum from the amorphous region. OPTIM was first used to create ''min.data.info'' files using ''odata'..." current
- 18:27, 10 May 2019 diff hist +1,761 N Running an Gaussian03 interfaced OPTIM job Created page with "To run a gaussian03 interfaced OPTIM job, you need three (or four, see below) files with names specified in the following list: (1) ''odata'' -- includes the keyword "'''GA..." current
- 18:27, 10 May 2019 diff hist +1,315 N Compiling and using OPTIM with QUIP Created page with "== Compiling OPTIM with QUIP == Provided the correct compiler and library modules have been loaded as described here, compilation can be..." current
- 18:26, 10 May 2019 diff hist +9,800 N OPTIM and PY ellipsoids tutorial Created page with "== GMIN: Find some minima == First run GMIN to find the global minimum and a high energy minimum (or any two stationary points). == OPTIM: Finding a single pathway == Input:..." current
- 18:26, 10 May 2019 diff hist +2,783 N OPTIM/Q-Chem Tutorial Created page with "== Setup Q-Chem == First ensure that Q-Chem is installed: if qchem gives Need at least to specify the input file. Usage: qchem [ -save ] [ -np procs ] infile [ outfile ]..." current
- 18:25, 10 May 2019 diff hist +10,712 N Visualising normal modes using VMD and OPTIM Created page with "In order to visualise normal modes in this way - you need to have done a harmonic normal mode analysis of the system using OPTIM. Details on how to do this can be found in the..." current
- 18:25, 10 May 2019 diff hist +469 N Perm-pdb.py Created page with "This program creates a ''perm.allow'' file from a pdb. The script is located here or in the svn repository under SCRIPTS/make_perm.allow/ . It is used..." current
- 18:24, 10 May 2019 diff hist +740 N Adding partially finished OPTIM stationary points to a PATHSAMPLE database Created page with "Sometimes a PATHSAMPLE run will end before all of the identified stationary points have been integrated into the databases files. These file can be found in the /scratch dire..." current
- 18:23, 10 May 2019 diff hist +125 N CAMSHIFT Created page with "Some notes on doing global optimization on CHARMM plus CAMSHIFT landscapes. * Keywords * Parameter-scanning script" current
- 18:23, 10 May 2019 diff hist +492 N GMIN TESTS module Created page with "'''This module is not yet implemented - if you want to do it - go right ahead!''' ==Introduction== This module is to be implemented in GMIN. It will contain tests of rou..." current
- 18:22, 10 May 2019 diff hist +2,449 N GMIN SANITY module Created page with "==Introduction== The GMIN SANITY module is intended to contain basic sanity check functions which can be used to help us check that we aren't doing anything stupid - for e..." current
- 18:22, 10 May 2019 diff hist 0 N File:Coding.jpg current
- 18:21, 10 May 2019 diff hist 0 N File:GMINflow.png current
- 18:21, 10 May 2019 diff hist +6,446 N GMIN MOVES module Created page with "==Introduction== Alongside the implementation of CUDA L-BFGS, we are currently in the process of re-working how GMIN takes 'steps', perturbing the coordinates before minimisin..." current
- 18:20, 10 May 2019 diff hist +921 N Amberinterface Created page with "Need to tidy this page up, but here's the basics. * The ix array stores '''all''' integers in AMBER, x array stores all floats in AMBER (e.g. charges, coordinates, masses), i..." current
- 18:20, 10 May 2019 diff hist +24,578 N Program flow Created page with "This page is intended to contain information about what the various files in GMIN do and what order they're called...." current
- 18:19, 10 May 2019 diff hist +2,600 N Progress Created page with "When run in a directory containing a ''GMIN_out'' file, it returns the % completion and hours remaining. Note that it is not entirely accurate as the time per quench is differ..." current
- 18:19, 10 May 2019 diff hist +3,187 N Makerestart Created page with "GMIN creates a file, ''GMIN.dump'' every 1000 steps which allows you to restart the run if, for example, your job crashed of if you simply want to run more quenches to see if..." current
- 18:18, 10 May 2019 diff hist +1,592 N Python interface for GMIN/OPTIM Created page with "= Introduction & Motivation = GMIN can be compiled as a python interface. Use the cmake option -DWITH_PYTHON. The goal of this interface is to allow for quick testing of new i..." current
- 18:18, 10 May 2019 diff hist +3,589 N Rotamer moves in AMBER Created page with "This page is for using rotamer moves with AMBER12 in GMIN. Rotamer moves convert side chains between stable conformations and should be paired with backbone group rotation mov..." current
- 18:17, 10 May 2019 diff hist +702 N PYGMIN & DMACRYS Created page with "PYGMIN (or minGMIN) is a python implementation of some of the important DMACRYS / OPTIM functionality. It has a strong focus on an object oriented & modular design which makes..." current
- 18:17, 10 May 2019 diff hist +2,559 N Keywords Created page with "=== List of keywords (to go into a data file) that may be useful: === CAMSHIFT <various parameters> ! turn camshift on CHARMM and CHARMMTYPE <> ! camshift only plays..." current
- 18:17, 10 May 2019 diff hist +1,218 N DMAGMIN setup Created page with "= Compiling DMAGMIN = DMAGMIN can only be compiled using cmake. I do not plan to add a target to the makefile. Steps to compile # Get DMACRYS and place it in svn. There are s..." current
- 18:16, 10 May 2019 diff hist +5,826 N Biomolecules in the energy landscape framework Created page with "This page is intended to collect information how the potential energy landscape framework can be used for biomolecules. Some information is provided directly on this page, and..." current
- 18:15, 10 May 2019 diff hist +11,478 N Mutational BH steps Created page with "This wiki describes mutational BH steps as they are implemented for AMBER12 within GMIN. The tutorial contains two parts - a description of how to use the mutational steps and..." current
- 18:15, 10 May 2019 diff hist +1,679 N Generating a GMIN Eclipse project Created page with "Eclipse is an IDE which offers support for fortran via the photran module. CMake can automatically generate Eclipse projects using the following line cmake -G "Eclipse CDT4..." current
- 18:14, 10 May 2019 diff hist +4,492 N Using GMIN and OPTIM with GPUs Created page with "== Compilation == CUDAGMIN and CUDAOPTIM can be compiled using CMake and both include the AMBER 12 code without selecting this as an additional compilation option. The AMBER d..." current
- 18:14, 10 May 2019 diff hist +3,876 N Compiling and using GMIN with QUIP Created page with "== Checking out the QUIP code == The necessary compilers and libraries for the QUIP interface are currently only available on Dexter, Sinister and Volkhan. Access to the QUIP..." current
- 18:12, 10 May 2019 diff hist 0 N File:Naotvside.png current
- 18:12, 10 May 2019 diff hist 0 N File:Naotvtop.png current
- 18:11, 10 May 2019 diff hist +11,806 N Ligand binding-mode searches with HBONDMATRIX Created page with "==Introduction== '''HBONDMATRIX''' is a new (AMB)GMIN keyword which changes the way GMIN function to improve the sampling of ligand binding-modes in large protein systems..." current
- 18:10, 10 May 2019 diff hist +5,158 N Running a G\=o model with the AMHGMIN Created page with "GMIN can now incorporate the IMM1 implicit membrane model described by Themis Lazaridis [http://www3.interscience.wiley.com/cgi-bin/fulltext/104537101/HTMLSTART]. To use t..." current
- 18:10, 10 May 2019 diff hist +3,460 N Running a Go model with the AMHGMIN Created page with "GMIN can run various types of Go models with the AMH framework. This is useful for creating starting points for OPTIM, and also there are different forms of Go-like pote..." current
- 18:09, 10 May 2019 diff hist +5,158 N Using the implicit membrane model IMM1 Created page with "GMIN can now incorporate the IMM1 implicit membrane model described by Themis Lazaridis [http://www3.interscience.wiley.com/cgi-bin/fulltext/104537101/HTMLSTART]. To use t..." current
- 18:09, 10 May 2019 diff hist +2,961 N Restarting a GMIN run from a dump file Created page with "GMIN has a facility for restarting a run, as long as you have a GMIN.dump file. This means that if the job runs out of walltime, or you'd like to check if you really have..." current
- 18:09, 10 May 2019 diff hist +58,507 N Calculating binding free energy using the FSA method Created page with "The FSA approach is a method developed in the group to allow us to calculate the binding free energy for large protein-ligand systems efficiently. We achieve this by locally r..." current
- 18:08, 10 May 2019 diff hist +1,596 N Global optimization of biomolecules using AMBER9 with Structural Restraints Created page with "This if similar to running plain global energy optimisation. Here you can find examples of input files necessary to work with GMIN: 1. ''coords.inpcrd'' -- file with coordina..." current
- 18:08, 10 May 2019 diff hist +2,870 N Global optimization of biomolecules using AMBER9 Created page with "Here you can find examples of input files necessary to work with GMIN: 1. ''coords.inpcrd'' -- file with coordinates 2. ''coords.prmtop'' -- topology file (see [http://wwmm...." current
- 18:07, 10 May 2019 diff hist +16,664 N Global optimization of biomolecules using CHARMM Created page with "Upper Level: GMIN (Under construction -- just posting a note on GMIN CHARMM data file and a set of input files for testing. 21 Jun 2011) The data file being used for CH..." current
- 18:06, 10 May 2019 diff hist +1,219 N Selecting search parameters for GMIN Created page with "There are a few general tips for selecting parameters for geometry optimisation. 1. The number of '''STEPS''' should be long enough to at least see one conformational change..." current
- 18:06, 10 May 2019 diff hist +889 N Adding a model to GMIN Created page with "This is rough outline of the subrounties that need to be changed to add a new model to GMIN. Your mileage will vary a bit with respect to the details. '''main.F''' -- start..." current
- 18:05, 10 May 2019 diff hist +5,408 N Pele Created page with "pele is a package written mostly in python that reproduces some of the core functionality of GMIN, OPTIM, and PATHSAMPLE. It is not meant to be a replacement for them, but ra..." current
- 18:04, 10 May 2019 diff hist +4,961 N Running Wales Group software on Windows 7 Created page with "Running the Wales Group software on Windows 7 has not been thoroughly tested and is not officially supported. However, it is possible. This page describes downloading Cygwin,..." current
- 18:04, 10 May 2019 diff hist +30 Comprehensive Contents Page →Running on Windows
- 18:03, 10 May 2019 diff hist +2,144 N AMBER Created page with "'''Notes on AMBER 12 interface''' thumb|"The bugs have magically disappeared!"|200px|right [http://amber.scripps.edu/ "AMBER"] (Assisted Model Buil..."
- 17:59, 10 May 2019 diff hist +1,460 N CHARMM Created page with "[http://www.charmm.org CHARMM] (Chemistry at HARvard Macromolecular Mechanics) is a program capable of running all or united atom energy minimization, Molecular Dynamics and M..." current
- 17:59, 10 May 2019 diff hist +9,487 N Revamping the modules system Created page with "The large number of different compilers, maths libraries, and MPI suites on the clusters causes confusion. The modules system works quite well for switching between them (it's..." current
- 17:58, 10 May 2019 diff hist +5,638 N Installing python modules Created page with "Sometimes it is useful to install your own python modules rather than asking Catherine and Greg to add them to the sector image: either you want to play with the code, you wan..." current
- 17:58, 10 May 2019 diff hist +7,888 N Cmake interface building Created page with "== Overview == As we try to constantly add new potentials to our group code, it is necessary to interface these properly in such a way that: * 1. the interface is built corr..." current
- 17:57, 10 May 2019 diff hist +5,765 N Branching and Merging Created page with "==Branching== A branch is created in the repository by remotely copying one of the existing development streams (e.g. trunk) as follows: svn copy url-old url-new where, fo..." current