[gmx-users] NVT-Eq ---> NVT-MD

[Alexander Alexander]

Dear Mark,

To be honest, I do not know exactly when and in which physics the velocity
generation in a MD simulation is necessary and when not !

And I usually-historically generate velocity in the Equilibration and not
in Production.

My specific case here is a pure metallic surface.

Regards,
Alex

On Mon, Feb 15, 2016 at 6:27 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Why did your two-part run need to generate velocities at a suitable
> temperature in the first part? Does that reason apply to your one-part run?
> ;-)
>
> Mark
>
> On Mon, Feb 15, 2016 at 6:23 PM Alexander Alexander <
> alexanderwien2k at gmail.com> wrote:
>
> > Thanks for your prompt response,
> >
> > Could you please confirm me that  in my single NVT-MD I should  use
> > "continuation  = no" and below velocity generation, right? or velocity
> > generation is not required any more?
> >
> > ;Generate velocity
> > gen_vel = yes
> > gen_temp = 298.15
> > gen_seed = -1
> >
> > Regards,
> > Alex
> >
> > On Mon, Feb 15, 2016 at 6:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 2/15/16 12:09 PM, Alexander Alexander wrote:
> > >
> > >> Dear Gromacs user,
> > >>
> > >> I have an elementary question which I would be thankful if one could
> > >> comment on it;
> > >>
> > >> I want to do a NVT-MD simulation as a production calculation of my MD
> > >> simulation for 10 ns, and suppose that a NVT- Equilibration has been
> > done
> > >> in advance for 0.5 ns. The normal differences between their .mdp files
> > are
> > >> coming below and the rest of their .mdp files are fully identical;
> > >>
> > >> NVT-Eq (Equilibration)
> > >> ------------------------------------
> > >> nsteps  =  500000    ; 0.5 ns
> > >>
> > >> ;Generate velocity
> > >> gen_vel = yes
> > >> gen_temp = 298.15
> > >> gen_seed = -1
> > >> -------------------------------------
> > >>
> > >>
> > >> NVT-MD (Production)
> > >> -------------------------------------
> > >> nsteps = 10000000    ; 10 ns
> > >> continuation  = yes    ;continuing from NVT-Eq
> > >>
> > >>
> > >> ;Generate velocity
> > >> gen_vel = no
> > >> -------------------------------------
> > >>
> > >> Since they have identical .mdp parameters, then, my question is that:
> > >>
> > >> if it is possible to do just one NVT-MD simulation (a bit longer (10 +
> > >> 0.5)ns ) instead of two sequence NVT-Eq and NVT-MD simulations?
> > >>
> > >>
> > > Of course.  The normal use for separating two phases (equilibration and
> > > production) is in the case of restraints, shorter time step for
> > > equilibration in troublesome systems, etc.  If you just have the same
> > > settings, do a single run.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
> > > --
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