I have gone through Mark Abraham's tutorial on REMD http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B
Now I would like to run my own REMD, adjusted from Justin's Lysozyme tutorial (is this correct?) http://www.mdtutorials.com/gmx/lysozyme/index.html Can I ask, 1) The normal MD involves EM, NVT, NPT and production run, while the REMD in the tutorial involves Stage 1 of equilibration and Stage 2 of production run. Should I run normal MD for EM and NVT, and run REMD for NPT and production run? 2) How many steps should be used for the "-replex" option in the production run? The REMD tutorial uses 100, is this generally applicable? My protein is ~50 kDa. 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.
