[gmx-users] on crashed MD

Brett brettliu123 at 163.com
Sun Apr 3 05:37:04 CEST 2016

Dear All,

Before when I got a MD crashed, I do the following to continue it,

"gmx  tpbconv -s md_0_1.tpr -extend 0 -o md_0_1extending0ps.tpr
gmx mdrun -deffnm md_0_1extending0ps -cpi md_0_1_prev.cpt -reprod -v &"

Recently I have a crashed MD, and when I do "gmx  tpbconv -s md_0_1.tpr -extend 0 -o md_0_1extending0ps.tpr", it says tpbconv has been replaced by convert-tpr.

In "http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/onlinehelp/gmx-convert-tpr.html#gmx-convert-tpr", there was introduction on  convert-tpr, which says,

"gmxconvert-tpr can edit run input files in four ways.

1. by modifying the number of steps in a run input file with options -extend, -until or -nsteps (nsteps=-1 means unlimited number of steps)

2. (OBSOLETE) by creating a run input file for a continuation run when your simulation has crashed due to e.g. a full disk, or by making a continuation run input file. This option is obsolete, since mdrun now writes and reads checkpoint files. Note that a frame with coordinates and velocities is needed. When pressure and/or Nose-Hoover temperature coupling is used an energy file can be supplied to get an exact continuation of the original run.

3. by creating a .tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your .tpx file, or when you want to make e.g. a pure Calpha .tpx file. Note that you may need to use -nsteps-1 (or similar) to get this to work. WARNING: this .tpx file is not fully functional.

4. by setting the charges of a specified group to zero. This is useful when doing free energy estimates using the LIE (Linear Interaction Energy) method".

My first question is, when I meet a crashed MD, can I continue it by

"gmx  convert-tpr -s md_0_1.tpr -extend 0 -o md_0_1extending0ps.tpr
gmx mdrun -deffnm md_0_1extending0ps -cpi md_0_1_prev.cpt -reprod -v &"?

My second question is, as for the introduction on convert-tpr says to continue a crashed MD by "gmx  convert-tpr" was obsolete, will you please tell me the command by mdrun to directly continue a crashed MD?


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