[gmx-users] concatenating 2 xtc files

Justin Lemkul jalemkul at vt.edu
Thu Aug 1 19:23:22 CEST 2013

On 8/1/13 11:44 AM, Kavyashree M wrote:
> Sir,
> Thank you for the suggestion.. I will make use of it in
> future runs. but now the simulation is over.

But if something went wrong, then "over" is rather irrelevant, isn't it?

> There was some overlap of few ns in 8core machine.
> so while checking the rmsd plot there was a significant
> difference in rmsd between 8 core and 64 core overlapped
> region of simulation.

So your simulation started from some previous point and re-ran?  I don't see how 
this would be possible given what you have been posting.

> 1 more question is suppose I do not have checkpoint file
> and if I need to continue from a stopped point (not extending)
> does this command do the job?
> $ tpbconv -s old.tpr -f traj.trr -e ener.edr -o new.tpr
> Because when I tried with this there was a jump in the rmsd

That's why I asked before about checking the contents of the .tpr file.  You 
need to verify what it is exactly that you're doing and identify sources of 
potential problems.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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