[gmx-users] What is the "gen-vel" used for?

[Sun Yeping]

I guess I understand what you mean, but could you clarify it further? I
usually perform the simulations by the following process:

(1) energy minimization (EM); (2) NVT for 1 ns with heavy atom restraints;
(3) NPT for 1 ns with heavy atom restrains; (4) production simulation
without restraints.

To prove repeatability, I think I need to set up several parallel
simulations. Could I perform the NPT step for 3 different durations such as
1 ns, 2 ns, 5 ns to get three different velocities at the final frame of
the three NPT simulations, and remove the restraints and continue the
simulation from these velocities respectively? Thus I will get three
production simulations start from different velocities.

Or do I need to stop a so-called production simulations (without restraint)
at different time points and get three configurations, and repeat the EM,
NVT, NPT and production simulation steps for the three configurations
respectively to get three independent trajectories?

Best regards,

Yeping

On Fri, Jan 3, 2020 at 9:50 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/2/20 8:25 PM, Sun Yeping wrote:
> > Hello Justin,
> >
> > Your reply is very helpful. I can understand the first method for proving
> > repeatablity: use a different initial configuration. But how to set the
> > different initial velocities with the same initial configuration if not
> > using the "gen-vel" option in the .mdp file for the production
> simulations?
>
> Again, you don't generate velocities at the outset of a "production"
> simulation. You're creating a randomized system that needs to be
> re-equilibrated. Hence, velocities are only ever generated at the outset
> of the first step of equilibration. Perhaps this is just a discrepancy
> in terminology, but one cannot justifiably start a "production"
> simulation (i.e. one in which data are collected) from a totally random
> state that may not even be stable.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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