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... According to you if not the implicit solvent method, then any suggestion you can give..
Thanx alot in the advance PRASUN (ASHOKA) Desire + stability = Resolution Resolution + Hard work = Success On Mon, Feb 10, 2014 at 8:34 PM, Justin Lemkul <[email protected]> wrote: > > > 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]. > -- 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].
