How to get random velocities?
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.
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@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.
On Aug 11, 2021, at 8:02 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
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>
Sorry, I put the wrong link there. Instead it should be the following (but you could just use Google to find it, like I did): <https://www.gromacs.org/Support>
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@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.
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participants (2)
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Elaine Meng -
Seera Suryanarayana