[gmx-users] Velocities from the .gro file

Mohamed Abdelaal m.b.abdelaal at gmail.com
Tue Apr 14 22:55:58 CEST 2020 

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
>> > > > >
>> > > > > ==================================================
>> > > > >
>> > > > > --
>> > > > > 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.
>> > >
>> > --
>> > 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.
>
>

More information about the gromacs.org_gmx-users mailing list