Adding example input for Wales group programs
In order to make the GMIN, OPTIM and PATHSAMPLE software really usable to people outside the group, it is vital that functional, annotated input for the different applications of each is available on the web for people downloading the source to make use of. It will also help you within the group (or sector) when you want to start using a different program - to have some working example input available.
As of April 2nd 2009, the examples are being stored in:
arwen:/home/wales/www-wales/examples/<PROGRAM>/<EXAMPLE NAME>/<ARCHIVE>
for example:
arwen:/home/wales/www-wales/examples/OPTIM/normalmodes/COPTIMnormalmodes.tar.bz
This translates to a URL of http://www-wales.ch.cam.ac.uk/examples/OPTIM/normalmodes/COPTIMnormalmodes.tar.bz
Here are some guidelines for making examples to try and keep the format relatively consistent.
- Each set of input should be tested with the latest SVN version of the code - not your personal version. Make sure any changes you have made are committed to the repository and you have run svn update before testing.
- Each archive should contain a README file that details each input file and describes their role. This file should also contain information on which version of the code it has been tested for. This can be found by doing svn info in the source directory for the appropriate program. For example:
!-----------------------------------------------------------------------------! ! EXAMPLE COPTIM INPUT - single minimum normal mode analysis of met-enkephalin! ! Tested for r15589 of COPTIM (01/05/09) ! !-----------------------------------------------------------------------------! This archive contains all you need to perform a normal mode analysis of met-enkephalin and produce a variety of output files. It contains: * odata - OPTIM input file including the CHARMM input required to read in the input file * input.crd - CHARMM coordinate input file for metenk * output/ - directory containing the expected output * README - this file! The visualisation of the output produced by this analysis is described in a different example archive. Please direct any comments, bug reports or questions to Chris Whittleston (csw34@cam.ac.uk)
- The input files that are changable i.e. data, odata, odata.connect etc should be fully commented describing why each keyword has been used. How you do this is of course up to you, but one suggested way is as follows:
COMMENT !-----------------------------------------------------------------------------! COMMENT ! EXAMPLE COPTIM INPUT - single minimum normal mode analysis of met-enkephalin! COMMENT ! Tested for r15589 of COPTIM (01/05/09) ! COMMENT ! ! COMMENT ! To use you will need to change the paths indicated by 'CHANGE-->' to reflect! COMMENT ! your installation of the group software. ! COMMENT !-----------------------------------------------------------------------------! COMMENT <KEYWORD SUMMARY> COMMENT DEBUG : DEBUG included to give you more output to look at COMMENT SEARCH 0 : Perform an LBFGS minimisation converging the root mean square gradient to 10^(-6) COMMENT BFGSMIN 1D-6 : Dump all (ALLVECTORS) mass-weighted (MWVECTORS) Hessian eigenvectors (the normal modes) to vector.dump with COMMENT frequencies in cm-1. Also dump PDBs describing the per atoms and per residue displacement resulting from the action COMMENT of these vectors. COMMENT DUMPVECTOR ALLVECTORS MWVECTORS : Set kT in cm^(-1) to 212.67 corresponding to the temperature in the upper respiratory tract of COMMENT humans. This is used to Boltzmann weight the atomic and residue displacements caused by thermally COMMENT accessible normal modes (defined by frequency < kT) COMMENT KTWN 212.67 : Dump modes 1, 2 and 10 to individual PDB files for later visualisation COMMENT DUMPMODE 1 2 10 : Dump modes 1, 2 and 10 to individual PDB files for later visualisation COMMENT DUMPSTRUCTURES : Specifies that final structures should be dumped for the runs into pdb and xyz formats COMMENT STEPS 2000 : Do up to 2000 steps of optimisation COMMENT CHARMMTYPE toph19_eef1_perm.inp param19_eef1_perm.inp : Specify the CHARMM topology and parameter files to use - also sets the type COMMENT of CHARMM forcefield used to CHARMM19 (united atom) COMMENT CHARMM : Everything below the CHARMM line above is part of a CHARMM input file DEBUG SEARCH 0 BFGSMIN 1D-6 DUMPVECTOR ALLVECTORS MWVECTORS KTWN 212.67 DUMPMODE 1 2 10 DUMPSTRUCTURES ...
- The output created when the input is run should be included in the archive in a directory called output
The archive itself can be created by running the following command in the directory containing the input files, README and the output directory.
tar cvfj <ARCHIVE>.tar.bz *
Once this archive has been produced, please email it along with a brief description of what it does to Chris (csw34) and I'll get it up on the website. An example of....example input can be found for OPTIM here