[Chimera-users] How to get random velocities?

[Elaine Meng]

Hi Surya,
This e-mail address is for Chimera questions... we are not experts in other programs.

For Gromacs, see its own documentation, help archive, etc.
<https://manual.gromacs.org/current/user-guide/mdp-options.html>

I can only say that molecular dynamics (MD) means that the atoms are moving, so they have velocities.  There are several methods for assigning and adjusting the velocities in MD.  

In the Gromacs MD documentation try searching for "velocity generation" and "velocity" to see all those parameters.
<https://manual.gromacs.org/current/user-guide/mdp-options.html>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Aug 11, 2021, at 2:58 AM, Seera Suryanarayana via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear chimera users,
> 
> Dear VMD users,
> I was asked to do simulations five times with the same starting structure and number of processors. But the velocities should be different. Here my query is "How do you generate velocities in the gromacs?".
> 
> I request you to guide me how to do it.
> 
> Thanks in advance
> Surya
> Graduate student
> India.