[gmx-users] Restarting the job

Mark Abraham mark.abraham at anu.edu.au
Fri Aug 13 05:16:53 CEST 2010

----- Original Message -----
From: sonali dhindwal <sonali11dhindwal at yahoo.co.in>
Date: Friday, August 13, 2010 0:59
Subject: [gmx-users] Restarting the job
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

| -----------------------------------------------------------
| > Hello All,
> I have a query regarding the restarts of the jobs after crash.
> I want to simulate a protein for 2 ns but in between due to system shutdown, it stopped, and I made a restart using this command:
> mdrun -s topol.tpr -cpi state.cpt -appendnow I checked the rmsd of in between by producing a .xtc file of the job which ran till now and then checked g_rms of the simulation, it is showing a graph like this,(I have attached in the mail)

See http://www.gromacs.org/Documentation/How-tos/Graphing_Data for a couple of gnuplot tips. I suspect the weirdness is gnuplot interpreting something as data that it should not interpret as data, and that the contents of the .xvg are actually the second half of normal RMS variation.
> this is showing rmsd after the point the  job was restarted with some error in the beginning.
> I want to know if there will be error at the end of the job too in the output file, .gro ?

The final .gro will have the final coordinates, as normal.


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