[gmx-users] concatenate NAMD trajectories
kanaan at zedat.fu-berlin.de
Thu Aug 14 15:16:39 CEST 2014
thanks a lot for your quick reply, but I still have a doubt about how to
"translate" my trjcat command to trjconv:
trjconv -t0 -timestep XX -f one.dcd two.dcd three.dcd -o total
what do I need to add instead of "-t0"?
should I add my timestep instead of XX (in ps)?
> 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
>> 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
> 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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