Re: [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 



On Sat, Mar 10, 2018 at 20:56, Justin Lemkul
 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

jalem...@vt.edu  | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [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. 

Sent from Yahoo Mail on Android 
 
  On Sat, Mar 10, 2018 at 20:56, Justin Lemkul 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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] -sep option

[Justin Lemkul]

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Gromacs Users mailing list

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[gmx-users] -sep option

[Mansoureh Shahbazi]

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
-- 
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