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

[Sun Yeping]

On Tue, Dec 31, 2019 at 12:22 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/30/19 11:11 PM, sunyeping wrote:
> > Hello Justin,
> >
> > Thank you for your reply.
> >
> > If I need to prove the repeatability of a phenonmenon (such as the
> > peptide folding pathway or a conformational transition) in
> > simulations, is it reasonable to run the production MD several times
> > and each time the simulation is continued for the same NPT
> > equilibration? Do I need to introduce centain random factors (if not
> > the velocity) in each production simulation?
> >
>
> No, because those aren't independent observations. You're just running
> the same .tpr file over and over again, which will diverge slightly for
> numerical reasons but these are not true replicate simulations. If you
> want to prove repeatability, you need to repeat exactly what you did in
> the first case multiple times, with the only difference being either (1)
> a different initial configuration or (2) the same configuration with
> different initial velocities. The initial condition is what needs to
> change, and then you need to equilibrate and perform the simulation the
> same way to see if the same behavior arises.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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>
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