Hi, everyone: I am testing some transition path sampling (TPS) algorithms using GROMACS. For certain type of TPS methods, such as the weighted ensemble method, it requires to restart multiple simulations from a checkpoint and those simulations needs to be stochastic. In other words, the trajectories generated from the same checkpoint must be different from each other.
I am wondering what is the best way to do this. Suppose the overdamped Brownian dynamics (bd) thermostat is used, I think one can just start (not restart) multiple simulations with different random seeds from the structure of the checkpoint because the previous velocities do not matter. If the Langevin thermostat (sd) is used, is it possible to specify the random seed when restarting a simulation? Your advice or suggestions will be much appreciated and welcomed. Thank you. Bin W. Zhang -- 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.
