[gmx-users] Velocities from the .gro file

[Mohamed Abdelaal]

I have one more question please regarding the velocity.

What is the mean value for the velocity being generated by GROMACS ? Is it
zero ?

I have also understood fr om the below paragraph which is written in the
manual section 3.4.1, that the values generated are selected from the range
between 0 and 1, However I have opened my nvt.gro file and I have found
negative values for the generated velocity. How come that I have negative
values for the velocity if the generated velocity is within the range from
0-1 as written in the manual ? Am I missing something?

"If velocities are not available, the program can generate initial atomic
velocities  at a given absolute temperature T :
where k is Boltzmann’s constant (see chapter 2). To accomplish this, normally
distributed random
numbers are generated by adding twelve random numbers R k in the range 0 ≤
R k < 1 and
subtracting 6.0 from their sum. The result is then multiplied by the
standard deviation of the
velocity distribution kT /m i . Since the resulting total energy will not
correspond exactly to the
required temperature T , a correction is made: first the center-of-mass
motion is removed and then
all velocities are scaled so that the total energy corresponds exactly to T
(see eqn. 3.18)."

Many thanks,
Mohamed

On Wed, Apr 15, 2020 at 12:26 AM Eric Smoll <ericsmoll at gmail.com> wrote:

> My knowledge is a bit old.
>
> Tpr files are binary so you cannot read them without a special tool.  In
> gromacs 2018, there was a tool that would spit out the contents of a tpr
> file in a readable format.  Execute
> “gmx dump -h” to learn more.
>
> Justin is correct.  There is no tool or file that will allow you to add a
> constant velocity in the z direction to a set of atoms.  I would suggest
> writing a program to build a custom gro file from the start that has
> everything you want.  If that is not possible for you, you could use
> gen-vel and attempt to export a gro with the resulting velocities at some
> point afterward (e.g., use gen-vel tpr for a 1 step simulation writing
> coordinates and velocities to the trr at every step and then extract gro
> with velocities from the trr).  Then go through the gro file and add a
> constant z-velocity to all the atoms that need it.  Then read the edited
> gro file in again and proceed.
>
> -Eric
>
> Sent from my iPhone
>
> > On Apr 14, 2020, at 3:02 PM, Mohamed Abdelaal <m.b.abdelaal at gmail.com>
> wrote:
> >
> > 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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