[gmx-users] taking snapshots of the protein after simulation

Justin A. Lemkul jalemkul at vt.edu
Sat Jun 5 05:17:47 CEST 2010

Hassan Shallal wrote:
> Dear Gromacs users,
> I have had one of my studied proteins simulated in a 5 ns production.
> Now, I wonder how can I get, let's say, 100 coordinates files, each file 
> represent the coordinates of the protein at certain time during the 
> simulation, for example, each 50 ps OR.. What if I want these 100 files 
> to represent the most stable and least energetic conformations of the 
> protein during this 5 ns simulation independent of which time they 
> represent... I know that VMD can be used for that but I am not quite 
> sure how I can do it...
> Any hint or link or tutorial would be fully appreciated...

See trjconv -h, with special attention to the -dump, -skip, and/or -sep options.


> Thanks
> Hassan Shallal


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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