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 -Micholas ________________________________________ From: [email protected] <[email protected]> on behalf of Justin Lemkul <[email protected]> Sent: Monday, December 07, 2015 8:14 PM To: [email protected] 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 totally wrong. -Justin -- ================================================== 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 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
