[gmx-users] -sep option

Mansoureh Shahbazi shahbazi.2010 at rocketmail.com
Sat Mar 10 23:02:13 CET 2018

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. 

Sent from Yahoo Mail on Android 
  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 A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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


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