[gmx-users] Velocities from the .gro file

[Mohamed Abdelaal]

No, I use the generate velocity option in the .mdp files.

However I want now to assign different velocities in the x,y,z directions.
Which I thought it could only be done through the .gro file, but I don't
know If I did that, should I change the value of the generate velocity to
be = NO in the .mdp files ? (otherwise I would have generated the
velocities twice).

Moreover, if I added the velocities in the .gro file how can I generate the
velocities in the .gro file from a distribution (Maxwell) with a specific
mean and standard deviation ?

I have tried to search in different sources (the user list, manual, user
guide, research gate and other platforms) how to solve this velocity
problem but I didn't find a clear way to insert different velocities in the
x,y,z directions using distribution rater than constant velocities.

Please guide me how to do it as I am a little bit confused in the velocity
generation mechanisms.

Many thanks,
Mohamed

On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/6/20 12:16 PM, Mohamed Abdelaal wrote:
> > Hello everybody :)
> >
> > Can I use the gmx insert-molecules to insert molecules in my box with
> > velocities by adding the velocities in the .gro file and insert the
> > molecules from this .gro file ?
>
> Have you tried it?
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
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