[gmx-users] Basic GROMACS questions

[Justin Lemkul]

On 12/8/14 2:40 PM, Simone Bolognini wrote:
> Oh, ok! I should find a place where all these parameters are specified.

The primary literature for the force field is the best source.

> However: what you think about other paramteres? Are them ok?
>

Reasonable enough, but there's no need for nstlist = 5; it can safely be set to 
a higher value in most cases.  Also be sure to do a minimization without 
-DFLEXIBLE if you intend to use constraints.  Constraining flexible water can 
fail from time to time when you get weird geometries.

-Justin

-- 
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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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