[gmx-users] concatenating 2 xtc files

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

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

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