[gmx-users] concatenate NAMD trajectories

Justin Lemkul jalemkul at vt.edu
Thu Aug 14 15:09:19 CEST 2014

On 8/14/14, 9:04 AM, Natal Kanaan wrote:
> Dear all,
> I'm sure this is a simple question, but I'm having problems trying to
> concatenate trajectories obtained with NAMD.
> I used this command line:
> trjcat -f one.dcd two.dcd three.dcd -settime -o total.dcd
> and it asked me about the starting time of each chunk (wich is 0ps,
> 40000ps and 80000ps, to obtain a total of 100ns trajectory). It seems all
> correct but, when I try to compute, for instance, the rmsd, it can't
> because there is no time in the new "total.dcd".

Use trjconv -t0 -timestep or catdcd instead of trjcat; it should preserve time 



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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