[gmx-users] Velocities from the .gro file

[Mohamed Abdelaal]

Many thanks for your reply 😊

The limitation in the generate velocity using the .mdp file, is that while
I can generate the velocity from Maxwell distribution,  I will have the
same velocities in the x, y and z directions.

On the other hand, generating the velocity from the .gro file will let me
specify different velocities in the x,y and z directions but they will be
the same velocities for all the atoms (will not be taken from a maxwell
distribution with variation in the atoms velocities).

Is it possible to generate different velocities in the x,y and z directions
from a maxwell distribution ? (for example the velocities to be taken from
a maxwell distribution with a mean of 0.1 in the x direction and with a
mean of 0.2 in the y direction and with mean of 0.3 in the z direction?)

Thanks for your help :)
Mohamed

On Wed, Apr 8, 2020 at 05:48 Eric Smoll <ericsmoll at gmail.com> wrote:

> 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
> > > Lab: 303 Engel Hall
> > >
> > > Virginia Tech Department of Biochemistry
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalemkul at vt.edu | (540) 231-3129
> > > http://www.thelemkullab.com
> > >
> > > ==================================================
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List 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 or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List 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 or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List 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 or
> send a mail to gmx-users-request at gromacs.org.
>