[gmx-users] the changing of velocity in production stage

[Mark Abraham]

On Tue, Nov 26, 2013 at 2:47 PM, Mahboobeh Eslami <
mahboobeh.eslami at yahoo.com> wrote:

> dear mark
> I am very sorry.
> I did not understand your answer.
> please give a clearer answer.
>
> 1)do i set gen_vel= yes, gen_temp   = 300 and gen_seed   = -1  in all mdp
> file for
>  Equilibration and production or only in production stage.
>

I think you should equilibrate, take that output and use it as input for
your multiple copies with different velocity seeds, and then separately
re-equilibrate all of those (but you will not need as much time).

2)should I setother options  in the mdp file?
>

Not given your stated objective. continuation = whatever is fine, given
that you are equilibrating again.

Mark


>
> Thank you very much
>
>
>
>
> On Tuesday, November 26, 2013 2:56 PM, Mark Abraham <
> mark.j.abraham at gmail.com> wrote:
>
> Those are fine. I would equilibrate, then fork to do the generation, and do
> a shorter re-equilibration.
> On Nov 26, 2013 10:22 AM, "Mahboobeh Eslami" <mahboobeh.eslami at yahoo.com>
> wrote:
>
> > hi Dear Gmx Users
> >  i want to study the changing of velocity  in production stage, do i set
> > gen_vel= yes, gen_temp   = 300 and gen_seed   = -1  in all mdp file for
> > Equilibration and production or only in production stage? should I
> > setother options  in the mdp file.
> > Thanks a lot
> > --
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