User contributions for Adk44

10 May 2019

• 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
• 17:1717:17, 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
• 17:1717:17, 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
• 17:1717:17, 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
• 17:1617:16, 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
• 17:1517:15, 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
• 17:1517:15, 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
• 17:1417:14, 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
• 17:1417:14, 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
• 17:1217:12, 10 May 2019 diff hist 0‎ N File:Naotvside.png ‎No edit summary current
• 17:1217:12, 10 May 2019 diff hist 0‎ N File:Naotvtop.png ‎No edit summary current
• 17:1117:11, 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
• 17:1017:10, 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
• 17:1017:10, 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
• 17:0917:09, 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
• 17:0917:09, 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
• 17:0917:09, 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
• 17:0817:08, 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
• 17:0817:08, 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
• 17:0717:07, 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
• 17:0617:06, 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
• 17:0617:06, 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
• 17:0517:05, 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
• 17:0417:04, 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
• 17:0417:04, 10 May 2019 diff hist +30‎ Comprehensive Contents Page ‎ →‎Running on Windows
• 17:0317:03, 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..."
• 16:5916:59, 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
• 16:5916:59, 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
• 16:5816:58, 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
• 16:5816:58, 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
• 16:5716:57, 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