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- 17:15, 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
- 17:15, 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
- 17:14, 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
- 17:14, 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
- 17:12, 10 May 2019 diff hist 0 N File:Naotvside.png current
- 17:12, 10 May 2019 diff hist 0 N File:Naotvtop.png current
- 17:11, 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
- 17:10, 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
- 17:10, 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
- 17:09, 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
- 17:09, 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
- 17:09, 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
- 17:08, 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
- 17:08, 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
- 17:07, 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
- 17:06, 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
- 17:06, 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
- 17:05, 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
- 17:04, 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
- 17:04, 10 May 2019 diff hist +30 Comprehensive Contents Page →Running on Windows
- 17:03, 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..."
- 16:59, 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
- 16:59, 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
- 16:58, 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
- 16:58, 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
- 16:57, 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
- 16:55, 10 May 2019 diff hist 0 N File:Jenkins screenshot.jpg current
- 16:55, 10 May 2019 diff hist +5,650 N Jenkins CI Created page with "Jenkins CI is an open source tool for continuous integration. We use it to ensure GMIN, OPTIM and PATHSAMPLE are always working. Each night Jenkins downloads the latest cod..." current
- 16:33, 10 May 2019 diff hist +19,530 N ElaborateDiff Created page with "SVNDIFF taken from http://svn.sunbase.org/repos/svnutils/trunk/src/svndiff Put this in your ./bin/ directory. Make it executable. And you are set. ''svndiff --help'' will gi..." current
- 16:32, 10 May 2019 diff hist +17,313 N Compiling Wales Group codes using cmake Created page with "[http://www.cmake.org/ CMake] (Cross-platform Make) provides a simple, platform independent way for us to compile and test the group codebase. Dependencies are handled automat..."
- 16:32, 10 May 2019 diff hist +4,806 N Wales Group Version control Created page with "As of 16th July 2008, all the group code is under version control. GMIN, OPTIM and PATHSAMPLE, along with the CHARMM and AMBER code used with them have bee..."
- 16:31, 10 May 2019 diff hist +16,946 N SVN setup Created page with "The group code is now managed under Subversion (SVN) version control. What follows is a quick setup guide to get you up and running with the Wales Group codes - GMIN, OP..."
- 16:30, 10 May 2019 diff hist -32 Comprehensive Contents Page →Miscellaneous
- 16:30, 10 May 2019 diff hist +16 Comprehensive Contents Page →Miscellaneous
- 16:30, 10 May 2019 diff hist -35 Comprehensive Contents Page →Getting Started
- 16:28, 10 May 2019 diff hist 0 N File:Oakdene ropes.JPG current
- 16:27, 10 May 2019 diff hist 0 N File:Scafell Pike.JPG current
- 16:24, 10 May 2019 diff hist +11,415 N Wales Group Created page with "thumb|Ascent of Scafell Pike on the group holiday 2013|500px|right Image:Oakdene_ropes.JPG|thumb|Group photo with Victor's climbing ropes from the..."
- 16:21, 10 May 2019 diff hist -14 Comprehensive Contents Page →Getting Started
- 16:20, 10 May 2019 diff hist -255 Comprehensive Contents Page
- 16:15, 10 May 2019 diff hist +8 Main Page →Group Members Only
- 16:14, 10 May 2019 diff hist +105 Main Page
- 16:12, 10 May 2019 diff hist +141 Main Page →Members
- 16:12, 10 May 2019 diff hist -141 Main Page →Contact details
- 16:12, 10 May 2019 diff hist -3 Main Page →Members
- 16:10, 10 May 2019 diff hist +231 Main Page
- 15:48, 10 May 2019 diff hist +25,244 N Comprehensive Contents Page Created page with "This page is designed to organise all of the pages on this wiki, as well as provide other useful links. Note that some pages may appear under more than one heading. '''Broken..."
- 15:46, 10 May 2019 diff hist +190 Main Page
- 13:20, 9 May 2019 diff hist -5 Main Page
- 13:20, 9 May 2019 diff hist +5 Main Page
