[gmx-users] Velocities from the .gro file

[Eric Smoll]

On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal <m.b.abdelaal at gmail.com>
wrote:

> 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).
>

That sounds logical.  Set it to no if you provide your own initial
velocities.

>
> 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.
>
> There is a good section on this in the manual.  For example, section 3.4.1
in the Gromacs 5.1.2 manual.

Also, you know that the generate velocities option assigns velocities to
atoms from an approximate MB distribution at whatever temperature you
specify in the MDP file, right?  If I understand you correctly, the
generate velocities options should do exactly what you want.  With no extra
work.


> 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
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Office: 301 Fralin Hall
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> >
> > Virginia Tech Department of Biochemistry
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> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
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