[gmx-users] concatenating 2 xtc files
jalemkul at vt.edu
Thu Aug 1 13:48:43 CEST 2013
On 8/1/13 3:42 AM, Kavyashree M wrote:
> Dear Sir,
> First trajectory - traj1.xtc (0 to 5... ns)
> Second trajectory - traj2.xtc (5... to 25ns)
> But there is no gap in between.
> for concatenating -
> $ trjcat -f traj1.xtc traj2.xtc -o trajf.xtc
> For nujump -
> $ trjconv -f trajf.xtc -s md.tpr -pbc nojump -o trajf.xtc
> I also have a case where I ran 10ns in 64 cores and later
> continued in 8core machine. This also has the same problem.
> While running in 64 cores by default it did not generate
> the checkpoint file. So I has to use tpbconv to generate
> a new tpr file for continuing from the same point -
> $ tpbconv -s old.tpr -f traj.trr -e ener.edr -o new.tpr
I would suggest using gmxdump on new.tpr to verify that the coordinates it
contains are the same as the last frame in traj.trr.
Justin A. Lemkul, Ph.D.
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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