On 11/17/15 12:18 PM, Tuanan Lourenço wrote:
Hi, My name is Tuanan and I am a Ph.D Student from Brazil. I am trying simulate Li+ using the polarizable force field of Roux (J. Chem. Theor. Comput., (2010), 6, 774-786) but I don't understand how i create my Li+ structure PDB file. I must insert a Drude particle in Li+ PDB file??? Someone would have a tutorial or a example of PDB file of monovalent ion with polarizable force field based on Drude?
The initial coordinates of the Drude particle are the same as the parent atom. Following minimization and/or propagation in dynamics, the Drude moves in response to the surrounding environment.
Have a look at http://mackerell.umaryland.edu/charmm_drude_ff.shtml if you want the latest features for simulating polarizable systems. It's not in an official release (it's on my still-too-long to-do list) but the instructions are there, as well as sample .mdp files. The code has a modified genion that inserts polarizable ions for you, though this is really a trivial operation, as noted above.
-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 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.
