[gmx-users] Setting different intial velocities

[Justin Lemkul]

On 8/30/17 6:33 AM, Apramita Chand wrote:
> Dear All,
>   While doing NVT equilbration, I'm setting gen_seed=-1,gen_vel=yes and
> following it up with NPT equilibration(gen_vel=no) and MD (gen_vel=no).
> So if I want to generate different starting conditions by giving initial
> velociies differently, I should modify my NVT.mdp file and change the
> gen_seed. Is this procedure correct?

By specifying -1 as the seed, you're telling grompp to use a different 
number every time (it's based on the process ID of the command in the 
shell).

> Is there any standard values to pass on to gen_seed or any number will do?

There is no such thing as a standard value for a random seed.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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