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

[Mark Abraham]

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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