[gmx-users] Output velocities and forces for each step?

[Justin Lemkul]

On 1/26/18 4:15 AM, Mohd Farid Ismail wrote:
> Is there a way to split the coordinates, velocities, and forces into 
> separate .trr files?

Not that I know of, since coordinates are always there, but if you have 
a .trr with x, v, and f from mdrun, you can write .trr files that have 
x+v and x+f with trjconv, with -novel or -noforce options.

-Justin

> -- 
> Mohd Farid Ismail
> 26.01.2018, 15:00, "Mohd Farid Ismail" <mohd.farid.ismail at yandex.com>:
>> That does it. Thank you for your quick reply.
>> -- 
>> Mohd Farid Ismail
>> 26.01.2018, 13:19, "Shrinath Kumar" <shrinath.kumar at ucdconnect.ie 
>> <mailto:shrinath.kumar at ucdconnect.ie>>:
>>>
>>> 1. No, they are written at whatever frequency you specify in your 
>>> mdp file.
>>> Look at the nstxout, nstvout and nstfout options. You can choose to 
>>> write
>>> them to the .trr file at each step if you wish.
>>> 3. You can use gmx traj -ov -of
>>>
>>> On 26 January 2018 at 04:55, Mohd Farid Ismail 
>>> <mohd.farid.ismail at yandex.com <mailto:mohd.farid.ismail at yandex.com>
>>>
>>>      wrote:
>>>
>>>      Hi,
>>>
>>>      I don't understand the documentation about the .trr file. The
>>>     manual
>>>      mentions that the .trr file contains the coordinates and
>>>     velocities, and
>>>      optionally the forces. A few quetions:
>>>      1) Does this mean that the velocities are written at each step
>>>     just like
>>>      the coordinate, and that the information is written to the .trr
>>>     file?
>>>      2) What switch to the mdrun do I use to have the forces for
>>>     each step are
>>>      written to the .trr file?
>>>      3) How can one extract these velocities and forces into
>>>     separate files?
>>>
>>>      I've googled a little bit but couldn't find any definitive
>>>     information.
>>>
>>>      --
>>>      Mohd Farid Ismail
>>>
>>>
>>>
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>
>

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

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