[gmx-users] genion with Na or Ca

[Smith, Micholas D.]

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-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: Tuesday, January 12, 2016 7:41 AM
To: gmx-users at 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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