[gmx-users] sampling conformation on the basis of RMSD value

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 17 18:42:14 CEST 2008

vivek sharma wrote:
> Hi There,
> I have a 5 nsec trajectory file for my system...and a RMSD plot for the 
> same.
> while doing simulation I have sampled the frame at each 500 ps,
> Now I want to choose conformation on the basis of RMSD values, like 
> conformation which has RMSD difference of some value say A nanometer.
> Can anybody suggest me a way to do the same ?
> I heard of g-cluster command for the same, but don't know how can I use 
> it for given RMSD difference ?

The logfile printed out by g_cluster gives clusters of structures based on their 
RMSD, with the constituent members printed out next to the cluster number.  The 
cluster members are shown in terms of the timeframe corresponding to the frame.

You can then extract any frames you wish using trjconv -dump.


> Can I do it before giving the final run command, so it will sample the 
> conformation during the run on the basis of RMSD value ?
> With Thanks,
> Vivek
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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