[gmx-users] Velocities from the .gro file

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
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