User contributions for Adk44

13 May 2019

• 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
• 17:2717:27, 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
• 17:2717:27, 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
• 17:2717:27, 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
• 17:2617:26, 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
• 17:2617:26, 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
• 17:2517:25, 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
• 17:2517:25, 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
• 17:2417:24, 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
• 17:2317:23, 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
• 17:2317:23, 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
• 17:2217:22, 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
• 17:2217:22, 10 May 2019 diff hist 0‎ N File:Coding.jpg ‎No edit summary current
• 17:2117:21, 10 May 2019 diff hist 0‎ N File:GMINflow.png ‎No edit summary current
• 17:2117:21, 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
• 17:2017:20, 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
• 17:2017:20, 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
• 17:1917:19, 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
• 17:1917:19, 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
• 17:1817:18, 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
• 17:1817:18, 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