[gmx-users] extending umbrella sampling runs

Poojari, Chetan c.poojari at fz-juelich.de
Fri Oct 28 17:27:05 CEST 2011


I want to extend the umbrella sampling runs and have used the below commands:

 1) grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n index.ndx -o umbrella0.tpr

2) mdrun -s umbrella0.tpr -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -cpo 0.cpt -c 0.gro -x 0.xtc -g 0.log -e 0.edr

#extending the runs:

3)  tpbconv -s umbrella0.tpr -extend 15000 -o umbrella_20ns_0.tpr

4) mdrun -s umbrella_20ns_0.tpr -cpi 0.cpt -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -cpo 0_20.cpt -c 0.gro -x 0.xtc -g 0.log -e 0.edr

When i run the above mdrun command (4) I get the below error message. As I use  .xtc file for analysis, I have not written separate .trr output files for each window. By default it writes single traj.trr file for all my windows.

I removed the traj.trr file and carried out the mdrun step and i stil get the error message with traj.trr.

Please can i Know how do I get about extending this run.

Error message:

Output file appending has been requested,
but some output files listed in the checkpoint file 0.cpt
are not present or are named differently by the current program:
output files present: 0.log pullx-umbrella0.xvg pullf-umbrella0.xvg 0.xtc 0.edr
output files not present or named differently: traj.trr

Program mdrun, VERSION 4.5.3
Source code file: checkpoint.c, line: 2139

Fatal error:
File appending requested, but only 5 of the 6 output files are present.

Kind Regards,

Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt

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