[gmx-users] Velocities from the .gro file

Thu Apr 9 04:32:46 CEST 2020

On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal <m.b.abdelaal at gmail.com>
wrote:

> 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.
>

I think you mean "same velocity *distributions* in the x, y, and z
directions."  The distributions will be approximately the same but each
atom will have a different velocity.

>
> 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).
>

I think you mean "specify different velocity *distributions* in the x, y,
and z directions"

>
> Is it possible to generate different velocities in the x,y and z directions
>

I think you mean "generate different velocity *distributions* in the x, y,
and z directions."  If so, the answer is obviously yes. Because you can
type in each individual vxi, vyi, and vzi for every atom i, you can
generate different velocity distributions in the x, y, and z directions.

> from a maxwell distribution ?

I am not sure what this part of the sentence means.  If you do what you are
suggesting, you will not be working with a maxwell distribution because all
three directions should have identical distributions.  See comment below.
If there is another misunderstanding, you need to spend more time crafting
precise sentences to communicate what you are after.

> (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?)
>

In my last email I suggested reading section 3.4.1 of the manual version
5.1.2.  It seems you did not.  A 3D Maxwell Boltzmann velocity distribution
corresponds to three identical gaussian speed distributions in vx, vy, and
vz centered at zero (mean should be zero for vx, vy, vz).  Just change the
standard deviation of the velocity distribution sqrt(kT/m) for each
velocity component if you want them to be different.  If you don't want the
mean to be zero for whatever reason, add a constant.  However, a non-zero
mean for any of the velocity components will generate center of mass
motion.  If you want center of mass motion, turn off center of mass motion
removal in the mdp file.

> 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
> > > >
> > > > ==================================================
> > > >
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