[gmx-users] Velocities from the .gro file

[Mohamed Abdelaal]

Many thanks for your quick reply :)

On Tue, Apr 14, 2020 at 11:09 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/14/20 4:55 PM, Mohamed Abdelaal 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.*
>
> Presumably the authors used different software; GROMACS does not allow
> such granular control of velocities.
>
> > 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.
>
> That's not true. If you know what velocities you want to assign, do so
> *after* building the whole system by writing the velocities to the .gro
> file (you will need your own code/script to do this). Then do not
> generate velocities in the .mdp file and they will be read from the .gro
> 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)
>
> No, GROMACS has no such capability.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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