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

[Justin Lemkul]

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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