[gmx-users] how to extract individual frames from trajectory

[Justin Lemkul]

On 4/19/13 8:03 AM, aixintiankong wrote:
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> At 2013-04-14 11:07:39,aixintiankong <aixintiankong at 126.com> wrote:
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>   Dear,
>        I have made a 10ns prodution MD, I want to extract frames from the molecular dynamics simulations at regular intervals of 10ps and keep the file as individual pdb file. The  dt=0.002，nstxtcout   = 500，i want to use the follow command ,
>             trjconv -s topol.tpr -f traj.xtc -skip (number) -o conf.pdb -sep
> but i don't now how to set the number of skip,please help me.

Your .mdp settings suggest that you have saved frames every 0.1 ps.  Confirm 
with gmxcheck.  If you have frames every 1 ps and want output every 10 ps, then 
10/1 = 10 for the value of -skip.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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