[gmx-users] Minimization and Equilibration in PMF

[Justin Lemkul]

On 10/22/16 1:55 PM, Alex wrote:
> Dear gromacs user,
>
> I was wondering if all the minimization and equlibrations(NVT and NPT)
> which are necessary to be  done before every normal production run of MD,
> should also be done in each windows of umbrella sampling in order to have a
> good PMF curve? Or they can be waved and still have a good and reliable
> curve.
>

They're all just independent simulations and need to be treated as such.  If 
they're snapshots from a previous run, you might be able to forego minimization, 
but you should always equilibrate under the influence of the restraint potential 
before trying any actual data collection.

-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

==================================================