User contributions for Adk44

13 May 2019

• 10:3510:35, 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
• 10:3410:34, 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
• 10:3310:33, 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
• 10:3310:33, 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
• 10:3210:32, 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
• 10:3210:32, 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
• 10:3110:31, 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
• 10:3010:30, 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
• 10:3010:30, 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
• 10:3010:30, 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
• 10:2910:29, 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
• 10:2910:29, 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
• 10:2810:28, 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
• 10:2810:28, 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
• 10:2710:27, 13 May 2019 diff hist +533‎ N CamCASP/Programming ‎ Created page with "CamCASP => Programming == Programmers Notes == * Status * Basis functions * CamCASP/Programming/2 | The..." current
• 09:3209:32, 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
• 09:3209:32, 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
• 09:3109:31, 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
• 09:3109:31, 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
• 09:3009:30, 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
• 09:3009:30, 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
• 09:2909:29, 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
• 09:2909:29, 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
• 09:2809:28, 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..."
• 09:2709:27, 13 May 2019 diff hist 0‎ N File:Tamiflu.gif ‎No edit summary current
• 09:2709:27, 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
• 09:2609:26, 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
• 09:2609:26, 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..."
• 09:2509:25, 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
• 09:2509:25, 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
• 09:2409:24, 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
• 09:2409:24, 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
• 09:2309:23, 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
• 09:2309:23, 13 May 2019 diff hist +13‎ N Quasi-continuous interpolation for biomolecules ‎ Created page with "More soon ..." current
• 09:2209:22, 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
• 09:2109:21, 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
• 09:2109:21, 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
• 09:2109:21, 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
• 09:2009:20, 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
• 09:1909:19, 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
• 09:1909:19, 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
• 09:1909:19, 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
• 09:1809:18, 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
• 09:1809:18, 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
• 09:1709:17, 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
• 09:1709:17, 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
• 09:1609:16, 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
• 09:1509:15, 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
• 09:1409:14, 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

10 May 2019

• 17:2817:28, 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