Adding example input for Wales group programs
Revision as of 14:23, 2 April 2009 by import>Csw34
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
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
- The input files that are changable i.e. data, odata, odata.connect etc should be fully commented describing why each keyword has been used. For example:
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 ! DEBUG included to give you more output to look at DEBUG COMMENT ! Specify eigenvector-following (SEARCH) minimisation (0) SEARCH 0 COMMENT ! Perform an LBFGS minimisation converging the root mean square gradient to 10^(-6) BFGSMIN 1D-6 COMMENT ! Dump all (ALLVECTORS) mass-weighted (MWVECTORS) Hessian eigenvectors (the normal modes) to vector.dump with frequencies in cm-1 COMMENT ! Also dump PDBs describing the per atoms and per residue displacement resulting from the action of these vectors DUMPVECTOR ALLVECTORS MWVECTORS ...