On 11/18/14 10:44 AM, Carlo Martinotti wrote:
I'm trying to run a hamiltonian REMD simulation at constant temperature, but i have problems installing plumed with hrex as suggested by Bussi ( https://groups.google.com/forum/#!msg/plumed-users/ROngJ1UyfHI/-nlna83yTy0J ). The thing that i was thinking so is to prepare one topology for every replica with pertrurbed values of bonds, lenght, dihedral, charges etc, then make individual tpr files and then run the simulation with multidir and replex. The problem is that if i keep the temperature 300K for every replica, gromacs tells me that there is nothing to exchange and the simulation dies. So i was wondering, as gromacs needs different temperatures for starting the simulations, is it acceptable to "trick him" introducing for every replica a slightly different temperature (i have to run 32 replicas, i was thinking to run the first replica with unperturbed hamiltonian at 300K and then increment by 0.1 K every replica) ? Would this perturbation affect the exchange probability of 2 replicas significantly? Thank you in advance for your time!
I think it makes more sense to simply make use of the free energy code in this case to do the HREX. You can define any number of lambda states for scaling of LJ, Coulombic, bonded, etc. interactions and simply define each replica to be one of those lambda states. The replica exchange code works fine when you define different lambda states, even at the same temperature.
-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.
