On 10/7/14 10:59 PM, Kester Wong wrote:
Hi Justin, Thank you for the clarification. I should look into using NAMD. The new polarisable Drude implementation will surely benefit everyone in the MD community. I am looking forward to using it, as with others (I think there was a similar post by Yana Tsoneva on this issue too, dated back in July). Meanwhile, is it possible to implement a self-consistent FF from scratch? One example I came across is from the work by Ho and Striolo titled: Polarizability effects in molecular dynamics simulations of the graphene-water interface
Of course you can implement whatever you like. Gromacs has been able to carry out polarizable simulations for a very long time; I've only ever cautioned against abuse of certain models.
Pardon me if this sounds outright wrong; regarding the massless Drude particle, can it be replaced with an atom (assuming an induced dipole model) instead of the charge-on-spring model? The mass of the atom can be set to 0.4 amu with an opposite charge of the water oxygen atom?
In the Drude model with 0.4-amu particles, the Drudes are essentially just atoms. There's nothing conceptually special about them, we just handle them slightly differently in the code.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
