Hi,
On Wed, Jan 22, 2020 at 5:55 PM ZHANG Cheng <272699...@qq.com> wrote: > My purpose of running REMD is to generate sufficient conformation > sampling, and try to use them to explain the in vitro data at 65C (338.15K). > > > I am using the "Temperature generator for REMD-simulations" at > http://folding.bmc.uu.se/remd/ > > > I am not sure about the "standard/default" values of several parameters. > Can I ask how to determine them? > > > 1) Exchange probability: it should be a value between 0 to 1. The higher > of the value I set, the shorter intervals of the temperatures are > output. > > > For the definition of exchange probability (isobaric and isothermal ensemble) between 2 replicas i and j see eq 4 in http://manual.gromacs.org/documentation/2019-current/reference-manual/algorithms/replica-exchange.html?highlight=replica%20exchange Best regards Alessandra > 2) Tolerance: by default it is 1e-4. So I just use it? > > > 3) Lower/Upper temperature limit: As I am interested in 338.15K, should > the lower limit set to be 338.15K, while the upper limit as 373.15K > (i.e.100C)? Should it be even higher? > > > 4) Constraints in water: Fully flexible? > > > 5) Constraints in the protein: All bonds? > > > 6) Hydrogens in protein: All H? (what does this mean?) > > > Is there a general rule for the number of temperatures used in the REMD? > Please feel free to tell me if there is a guidelines for setting the > temperatures. > > > Thank you! > -- > 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. > -- 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.