On 2/10/14, 11:31 AM, prasun kumar wrote:
Dear All and Justin Thanx for the quick reply... My aim is to find the effect of the ion on the dodecamer (whether on adding ions it is stable or not) Seeing the system.. I am left with two options (My view): 1) Coarse Grain Method or 2. Implicit Solvent Method Coarse Grain Method is full of approximation thats why I was hesitant to follow this approach...
Well, implicit solvation is full of approximations, too.
According to you if not the implicit solvent method, then any suggestion you can give..
Hard to say. I think there are some significant limitations of MD in general in this case. As I said before, the representation of a metal ion as a simple sphere with charge +2 is a fairly poor approximation. The MD force fields do not reproduce effects like charge transfer or maintain proper coordination geometry without complex restraints. If absolutely nothing else, I think you need to use an explicit solvent model.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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].
