[gmx-users] Catenation and sampling

Justin Lemkul jalemkul at vt.edu
Thu Mar 2 23:08:56 CET 2017

On 3/2/17 11:40 AM, suniba shuaib wrote:
> Dear users and experts
> I have simulated a protein in water using OPLS-AA force field. Initially I
> performed a 5 ns simulation and then extracted frames out of it e.g. at
> 1ns, 2ns, 3ns etc. and then performed simulation for 100 ns of each
> extracted frame. Now I have five 100 ns trajectories (A.xtc, B.xtc, C.xtc
> etc..). My question is how should I catenate these trajectories in order to
> ensure good sampling. When I used gmx trjcat with -settime flag, I obtained
> RMSD and Rg which showed very high fluctuation till 150 ns and then was
> quiet stable till the end of 500ns. I am confused if these extra high
> fluctuations are due to poor sampling or improper catenation. Please help
> me.

You can easily resolve this by analyzing each trajectory separately (probably 
more appropriate in this case for such simple analysis) and also visualizing the 
trajectories.  If you've got one or more systems that are behaving differently, 
your best tool isn't written in code, it's your eyes :)


> The fluctuations in RMSD were between 0.2-1.8 nm till 150 ns and then RMSD
> stayed between 1.0-1.1 nm.
> With Regards
> Suniba


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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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