[gmx-users] extending umbrella sampling runs

[Justin A. Lemkul]

Poojari, Chetan wrote:
> Hi,
> 
> 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.
> 
> 
> 

If you have overwritten or deleted the traj.trr file(s), you cannot append. 
Either use mdrun -noappend or run your jobs such that either (1) you use a 
unique filename for the .trr files or (2) you set nstxout=nstvout=nstfout=0 so 
that the .trr file is not written at all.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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