[gmx-users] -sep option

[Mansoureh Shahbazi]

Dear justin, I want to make pdb files with regular intervals from a long trajectory.Can you please tell me an example command line using -sep? I want to get 100 pdbs from a 100 ns trajectory with 1ns (1000 ps) intervals. 

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  On Sat, Mar 10, 2018 at 20:56, Justin Lemkul<jalemkul at vt.edu> wrote:   

On 3/10/18 9:18 AM, Mansoureh Shahbazi wrote:
> Dear colleagues, How should I use -sep option to convert a frame of a trajectory to pdb? Can anyone send me the command line? Thanks

The -sep option is used to write a given interval of a trajectory into 
separate files. If you just want a single frame, you should use -dump 
and the corresponding time in ps.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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