[gmx-users] Velocities from the .gro file

Eric Smoll ericsmoll at gmail.com
Tue Apr 14 23:14:23 CEST 2020 

No problem.

Now it is clear what you are trying to do.  The previous description of
your goals did not make much physical sense.  The initial velocities are
such that all three dimensions are sampled from the same 3D velocity
distribution (gaussian with the same width).  The difference is that there
is a constant velocity added in the z-direction so there is net motion in
the z-direction.  One way to do this is to use gen-vel as usual and just
add the constant to the z-coordinate.

The velocities were probably read in.  By default, the velocities may not
be printed in the gro.  What matters is that they were loaded in the tpr.
Try a simulation to see if the molecule is moving as expected.
Alternatively, dump the contents of the tpr and make sure the velocities
you created were read in.

-Eric

On Tue, Apr 14, 2020 at 1:56 PM Mohamed Abdelaal <m.b.abdelaal at gmail.com>
wrote:

> Sorry for writing again in the same topic but I couldn't solve
> the velocity problem.
>
> I am trying to reproduce a paper written by: Claire Tonnel + , Martin
> Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, Alpeshkumar
> K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J.
> Powell
> Title: Elucidating the Spatial Arrangement of Emitter Molecules in Organic
> Light-Emitting Diode Films
>
> It was mentioned in the paper that " The molecule was inserted into the
> system such that the x and y coordinates of the centre of mass were sampled
> from a uniform distribution covering the entire box while the z coordinate
> of the centre of mass was set to 2.0 nm above the current surface. The
> initial orientation of the molecule was randomised. *The velocities of each
> atom within the inserted molecule in x and y were sampled from a Gaussian
> distribution with a mean of 0.0 nm/ps and a standard deviation appropriate
> for the temperature constant (σ = sqrt(kT/m), where k B is Botzmann’s , T
> is the temperature and m is the mass of the atom). The velocities in z were
> sampled from the distribution with the same standard deviation as x and y
> but with a mean of 0.05 nmps -1 , negative z velocities (molecule moving in
> the direction opposite to the surface) were rectified by taking the
> absolute value. This ensured all molecules moved toward the surface.*
>
> I have read the section 3.4.1 of the manual version 5.1.2 as recommended
> above and I have also read all the velocity related topics in the manual
> and user guide.
>
> (After Dr. Justin and Dr. Eric replies)  I added velocity in my .gro file
> and then I inserted the molecule in a box using insert-molecules, However
> after the insertion process is completed I opened the output .gro file but
> the velocity was not read. This means that I can only generate the velocity
> through the .mdp file.
>
> If I am going to generate the velocity using my .mdp file, is it possible
> to change the standard deviation and the mean ? if yes, how can I modify
> them ? (I can't find any way to modify the parameters of the Maxwell
> distribution)
>
> I want to have velocity distributions with means equal to 0,0,0.5 nmps in
> the x,y,z directions respectively.
>
> You wrote in your last email that, "A 3D Maxwell Boltzmann velocity
> distribution corresponds to three identical gaussian speed distributions in
> vx, vy, andvz 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."
>
> If the velocity will not be read from the .gro file where should I add the
> constant to change the mean?
>
> Many thanks,
> Mohamed
>
>
> On Thu, Apr 9, 2020 at 5:00 AM Mohamed Abdelaal <m.b.abdelaal at gmail.com>
> wrote:
>
> > 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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