[gmx-users] Velocities from the .gro file

[Mohamed Abdelaal]

Many thanks Dr. Erik for your reply :)


On Tue, Apr 14, 2020 at 11:15 PM Eric Smoll <ericsmoll at gmail.com> wrote:

> 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.
>

*Can you please tell me more details how to add the constant to the
z-coordinate ? If I will generate the velocity from the .mdp file, in which
file should I 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.
>

I will complete the simulation to the end to check whether or not the
velocity was added from my .gro file.


> Alternatively, dump the contents of the tpr and make sure the velocities
> you created were read in.
>
> Do you mean that I should manually edit the .tpr file ? I have tried to
open it with text editor but it can't be open.


> -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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