At low concentrations (just a single Ca2+) you shouldn't expect any huge differences, though the Ca2+ may stick around the protein surface a little bit longer than the Na+ ions which may alter how one of the charged residues is hydrated. If the protein is of a modest size (not a small fragment), than any modifications to the hydration of a single residue likely will not be a huge driving factor to your dynamics...though this is not guaranteed.
When in doubt, run both simulation conditions and compare. -Micholas =================== Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: Tuesday, January 12, 2016 7:41 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] genion with Na or Ca On 1/12/16 3:19 AM, Turgay Cakmak wrote: > Hi all, > > > I have a quick question about neutralizing the system. I have a solvated > system that contains a charged protein of -2q. Is there a major difference > betwen adding 2 Na ions and a single Ca ion to neutralize the system > (using genion)? > For the purposes of neutralization, probably not, but note that additive force fields do not deal well with divalent ions. Na+ or K+ are preferable if only being used for simple balancing of charge. -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 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org. -- 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 gmx-users-requ...@gromacs.org.
