[gmx-users] Force field selection for free Bicarbonate molecules in solution

Faulkner, Matthew M.Faulkner at liverpool.ac.uk
Fri Sep 4 15:14:10 CEST 2015

Thank you Justin,

I will check the charges. 

I appreciate the help.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: 04 September 2015 14:11
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

On 9/4/15 9:07 AM, Faulkner, Matthew wrote:
> Thank you Justin,
> Do you know a suitable force field to use for a topolgy from PRODRG? I am aware that the topology from PRODRG may now be of the best quality but I want to run a short MDS as proof of concept first to see if the events I am interested in occur in a  reasonable timeframe.

GROMOS.  Be sure to fix the charges that PRODRG gives you, otherwise any
simulation you run will have lots of artificial behavior.



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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