[gmx-users] -sep option

[Justin Lemkul]

On 3/10/18 4:52 PM, Mansoureh Shahbazi wrote:
> 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.
>

It's much easier with -dump, just loop over the desired time values in 
ps. Using -sep requires either -dt or -skip.

-Justin

> Sent from Yahoo Mail on Android 
> <https://overview.mail.yahoo.com/mobile/?.src=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
>
>     -- 
>     ==================================================
>
>     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 <mailto:jalemkul at vt.edu> | (540) 231-3129
>     http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
>     ==================================================
>
>     -- 
>     Gromacs Users mailing list
>
>     * Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
>     <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List%20>before
>     posting!
>
>     * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>     * For (un)subscribe requests visit
>     https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>     <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users%20>or
>     send a mail to gmx-users-request at gromacs.org.
>     <mailto:gmx-users-request at gromacs.org.>
>

-- 
==================================================

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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================