Hi Michael, I am just following up on your thoughts on how carrying out expanded ensemble at NVT and converting back to NPT on the mailing list. Again I appreciate your advice in this area.
Best wishes, Gregory On 5/8/2019 12:01 PM, Michael Shirts wrote: Yeah, this is an unfortunately place in the code where not all combinations work - very long story. Hopefully this will be working better in 2020. What I would recommend is, if possible, performing the expanded ensemble simulation at NVT. Everything should work fine there (paper coming out hopefully soon comparing a bunch of free energy methods). Once can always correct the free energy at lambda=1 from NVT to NPT. I Can fill in the details. You do NOT want to do Berendsen for NPT when running expanded ensemble. The results will be incorrect (as I have learned by sad experience_ On Wed, May 8, 2019 at 8:14 AM Gregory Man Kai Poon <gp...@gsu.edu><mailto:gp...@gsu.edu> wrote: Hi all: We are interested to do expanded ensemble simulations (such as simulated tempering) on GROMACS. Extensive fiddling with the settings and googling on other people's experience suggests that these simulations must use the md-vv integrator, which in turn is compatible with Berendsen or MTTK coupling for pressure. However, MTTK does not work with constraints, which are needed for the forcefields. Berendsen can handle constraints but is not recommended for preserving thermodynamic ensembles. Any ideas on how one should proceed? Many thanks for your thoughts. Gregory -- Gromacs Users mailing list * Please search the archive at https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Cgpoon%40gsu.edu%7C0691e8847a2b444b3a8208d6d3ce834d%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C1%7C636929281266198778&sdata=6gqdkFvDH2oX6U17pgPfcUvs34mmPP6OCyPnUQbgwKE%3D&reserved=0 before posting! * Can't post? Read https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&data=02%7C01%7Cgpoon%40gsu.edu%7C0691e8847a2b444b3a8208d6d3ce834d%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C1%7C636929281266198778&sdata=xJsYvSXLGH4aeubUlxygOvzszCraVOEywg%2BwFcnAIQA%3D&reserved=0 * For (un)subscribe requests visit https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=02%7C01%7Cgpoon%40gsu.edu%7C0691e8847a2b444b3a8208d6d3ce834d%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C1%7C636929281266198778&sdata=1zXWxg16PNlz5%2FFgFsmfO79eangf1sRB%2BkzpcuT3OFU%3D&reserved=0 or send a mail to gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org>. -- Gregory M. K. Poon, PhD, RPh Associate Professor Departments of Chemistry and Nutrition | Georgia State University NSC 414/415/416 | 50 Decatur St. SE, Atlanta, GA 30302 P.O. Box 3965 | Atlanta, GA 30303 Ph (404) 413-5491 | gp...@gsu.edu<mailto:gp...@gsu.edu> -- 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.
