[gmx-users] Choosing water molecules and box type and dimensions

Justin Lemkul jalemkul at vt.edu
Fri Apr 29 15:53:42 CEST 2016

On 4/29/16 9:51 AM, zeineb SI CHAIB wrote:
> Dear all,
> Thank your for your answers.
> @ Justin,
> Where can I found informations related to the compatibility of one water type with the force field that I choose for my protein? in other words "where can I found information about the water type that had been used for the parametrisation of my Force field"?

Read the primary literature for the force field you're using.  That's of course 
the first step, otherwise you wouldn't have chosen a force field yet, right? :)

Then look for subsequent citations of that force field in application studies 
related to water.  There are a few for each force field, but generally the water 
model is considered part of the force field and it is rare to deviate from this 
model.  Don't do it unless you have a really, really good reason.



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


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