[gmx-users] umbrella sampling with replica exchange
Hi, I have a technical question regarding feasibility of combining replica exchange with umbrella sampling or any other pulling simulations in gromacs. Since the umbrella sampling or any other pulling simulations are non-equilibrium simulation due to presence of external bias, I wonder whether the detailed balance in replica exchange simulation will be maintained . I ask this because replica exchange uses Monte Carlo metropolis algorithm to swap configurations and so I wanted to know what is the energy-difference ( New energy - old energy) in metropolis algorithm gromacs will use : Is it the energy difference after taking into account the biasing potential or is is only the internal potential energy-difference ( i.e not including biasing potential ) ? Any response from the users or developer will be highly appreciated. Thanks Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] umbrella sampling using replica exchange
Hi, I was wondering whether in gromacs 4, one can use replica exchange simulation in combination with umbrella sampling. Thanks Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] umbrella sampling using replica exchange
Sanku M wrote: Hi, I was wondering whether in gromacs 4, one can use replica exchange simulation in combination with umbrella sampling. In theory, yes. Whether or not it is efficient or stable is perhaps another matter. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
