[gmx-users] Velocities from the .gro file

Mohamed Abdelaal m.b.abdelaal at gmail.com
Thu Apr 9 05:02:00 CEST 2020 

Many thanks for your reply :)

All your language assumptions are true and that is exactly what I wanted to
communicate, next time I will try to be more precise and sorry for the
confusion 😊

I will read section 3.4.1 again carefully.

Thanks again and sorry for the inconvenience.

Mohamed

On Thu, Apr 9, 2020 at 04:33 Eric Smoll <ericsmoll at gmail.com> wrote:

> 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 t
> <https://www.google.com/maps/search/velocities+by+adding+the+velocities+in+t?entry=gmail&source=g>he
> .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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