[gmx-users] The mdrun can not continue to run from the last check point

Smith, Micholas D. smithmd at ornl.gov
Fri Nov 28 19:22:37 CET 2014

A  quick work-around is to take the last checkpoint and run tpbconv -f (your state-file here) -s (your tpr file here) -until (the end time you wanted) -o new.tpr

And start a new simulation (mdrun -s new.tpr -o md_new.trr -e md_new.edr -o md_new.log (other flags here) ).

When you are done with this additional run, you will need to use trjcat to combine your original trajectory with your new one and your set.

Micholas Dean Smith, PhD.
Post-doctoral Research Associate 
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of liuyong_1007 at dicp.ac.cn <liuyong_1007 at dicp.ac.cn>
Sent: Thursday, November 27, 2014 1:13 AM
To: Discussion?list?for?GROMACS?users
Subject: [gmx-users] The mdrun can not continue to run from the last check      point

Dear gmx users.

After been killed during the mdrun, the mdrun can not continue to run from the last check point.
The gromacs shows error as :
Program mdrun_mpi_d, VERSION 5.0
Source code file: /lustre/home/liuyong/gromacs-5.0/src/gromacs/gmxlib/checkpoint.c, line: 2218

Fatal error:
Can't read 404674 bytes of 'md.log' to compute checksum. The file has been replaced or its contents have been modified. Cannot do appending because of this condition.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
 The command line“mpirun.lsf mdrun_mpi_d -v -multidir sim* -s topol.tpr -cpi state.cpt -replex 500” are used.

liuyong_1007 at dicp.ac.cn
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