-n <name> | |
Specify a project name for using exclusive work_queue_worker instances. | |
-x <filename> | |
Specify the name of the xyz file for output. | |
-d <filename> | |
Specify the name of the dcd file for output. | |
-m <number> | |
Specify the number of monte carlo steps. Default = 100. | |
-s <number> | |
Specify the number of molecular dynamics steps. Default = 10000. | |
-p <path> | |
Specify path for storing output files. | |
-q | Assign closer temperature values to replicas in the first and last quartile. |
-l | Print debuggging information. |
-h | Show this help message. |
% setenv PYTHONPATH $HOME/cctools/lib/python2.4/site-packages
% replica_exchange_protomol ww_exteq_nowater1.pdb ww_exteq_nowater1.psf par_all27_prot_lipid.inp 278 400 84To run a replica exchange experiment, with project name ReplExch, over 250 Monte Carlo steps running 1000 molecular dynamics steps and involving 84 replicas in the temperature range 278 to 400K using the sample input files:
% replica_exchange_protomol -N ReplExch -m 250 -s 1000 ww_exteq_nowater1.pdb ww_exteq_nowater1.psf par_all27_prot_lipid.inp 278 400 84