On 2/10/14, 7:47 AM, prasun kumar wrote:
Dear All I am planning to study the effect of adding the ions on the dodecamer protein. For this purpose I need to add ions (Fe2+) in the system. Any suggestion for it. I have come to know through various discussion forums that there is no need of adding ions to make the system neutral, but in my case I have to add ions, how will be mdp file look for ions added system.
You wouldn't use genion in this case. In the case of implicit solvent, there's nothing to delete to replace with the ions. genbox -ci -nmol is what you want here, though it is questionable whether this sort of representation is at all meaningful. Hydrated ions (especially transition metals) have very complex properties. I'd suspect in an implicit solvent system, a lot of the behavior will not represent reality.
-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].
