[gmx-users] using SPC water with Charmm FF
Smith, Micholas D.
smithmd at ornl.gov
Tue Dec 8 14:32:56 CET 2015
I would mildly disagree with Justin on this one. Although Charmm should ideally be used with TIP3P (as Justin noted being one of the force-field developers and all), there have been a number of papers that show that SPC/E is not entirely incorrect (see below). What you would need to do is see if there is any experimental evidence you can compare to as a sanity check; though, many of the papers I cite below do indicate that SPC/E does still get the overall dynamics correct even when used with Charmm.
Citations of interest.
Force-Field Induced Bias in the Structure of Aβ21-30: A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force-Fields. DOI: 10.1021/acs.jcim.5b00308
Structure of Aqueous Proline via Parallel Tempering Molecular Dynamics and Neutron Diffraction. DOI: 10.1021/jp0714973
Testing the inter-operability of the CHARMM and SPC/Fw force fields for conformational sampling. DOI: 10.1080/08927022.2013.824574 (note* this is an SPC/E derivative water model, you milage may vary)
Local Order, Energy, and Mobility of Water Molecules in the Hydration Shell of Small Peptides. DOI: 10.1021/jp909090u
Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models. DOI: 10.1021/acs.jpcb.5b02937
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: Monday, December 07, 2015 8:14 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] using SPC water with Charmm FF
On 12/7/15 6:59 PM, jhon espinosa wrote:
> Hi allI finished running the 50 ns MD Simulation of a very large system (17 Million atoms).It is a capsid in water. I used charmm FF for the protein and spc for the water.I am studying temperature triggered structural transitions.Since Charmm FF is build based on TIP3p water model, are my simulation results wrong?Is there any main issue that I should know?ThanksJohn
Sorry to say that is an invalid physical model. The balance of forces will be
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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