On 01/04/2011, at 6:29 PM, Mark Abraham wrote:
On 1/04/2011 6:03 PM, Ruchi Gupta wrote:
Dear gmx-users,
I am facing some problems while running replica exchange MD using
Gromacs.
Few seconds after the job submission it ends with the following
error message:
"
Initializing Replica Exchange
Repl There are 6 replicas:
Multi-checking the number of atoms ... OK
Multi-checking the integrator ... OK
Multi-checking init_step+nsteps ...
init_step+nsteps is not equal for all subsystems
subsystem 0: 0
subsystem 1: 50000
subsystem 2: 0
subsystem 3: 50000
subsystem 4: 0
subsystem 5: 50000
-------------------------------------------------------
Program mdrun, VERSION 4.5.4
Source code file: main.c, line: 249
Fatal error:
The 6 subsystems are not compatible
For more information and tips for troubleshooting, please check the
GROMACS
website athttp://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"
I am using a "single .gro file" and "6 different md.mdp" files (at
6 different temperatures) for generating "6 .tpr files",
respectively. But the simulation doesn't work.
I have compared the ".tpr files" using "gmxdump" and "gmxcheck"
Gromacs commands and they seem fine with respect to nsteps and
init_step information.
So, to be clear, gmxcheck says that for no pair of .tprs does
init_step or nsteps differ...
What is your mdrun command line? Are you using checkpoint files?
Mark
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1) Comparison of the .tpr files using gmxdump reveals no differences
but for the temperatures and the velocities in each i.e. init_step and
nsteps have the same values (0 and 50000, respectively) in all files.
2) We have tried running mdrun without checkpointing (-cpt -1) and
with checkpointing with no change in the outcome.
Regards
Brian
Dr Brian J Smith
The Walter & Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Victoria 3052, Australia
Ph: +61 (0)3 9345 2687 Fax: +61 (0)3 9345 2686
http://www.wehi.edu.au/brian_smith
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