[gmx-users] Choosing water molecules and box type and dimensions
Smith, Micholas D.
smithmd at ornl.gov
Fri Apr 29 16:22:05 CEST 2016
Just to add, a study (http://pubs.acs.org/doi/full/10.1021/acs.jcim.5b00308 ) comparing the 7 force-fields and 3 common water models (for each force-field, except gromos) and found that at least for sampling protein behavior, TIP3P, TIP4P, and SPC/E can all be interchanged between Charmm27, OPLSAA, and Amber force-fields with only minor deviations from one another; i.e. if you compare water models for a given force-field the differences are fairly small.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of abhijit Kayal <abhijitchemiitd at gmail.com>
Sent: Friday, April 29, 2016 10:07 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Choosing water molecules and box type and dimensions
Justin, as always is absolutely right. The paper that I have suggested is
just compare the different water models with the bulk properties. And the
bio molecular forcefields are compatible with particular type water
model. Like charmm force field is compatible with TIP3P water.
On Fri, Apr 29, 2016 at 6:53 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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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