There is no rule regarding how many thermostats per system one needs. Often people choose separate thermostats for parts of system, which exhibit different mobility. I do not see any connection to functional forms of the interactions and, therefore, to force fields.
Dr. Vitaly V. Chaban On Thu, Jun 12, 2014 at 2:33 PM, 陈功 <gchen...@gmail.com> wrote: > Thanks a lot, Justin. I do CG simulation using Martini force field. So maybe > I can find some useful infomation on the forum of martini. > Thanks :) > > > > > > From: Justin Lemkul > Date: 2014-06-12 17:44 > To: gmx-users > Subject: Re: [gmx-users] how many groups shall I use to control the > temperature? > > > On 6/12/14, 2:37 AM, 陈功 wrote: >> Dear justin, >> I have doubts that whether I should use two groups to control the >> temperature or just one since there are just 604 hundred Protein beads and >> 60000+ solvent beads. It is said that two groups are more accurate but when >> when i split them into two groups "Protein nonProtein", I found that >> fluctulation of temperature in group "Protein" are obvious, Im afraid that >> would have an effect on accuracy on my simulation results. So how many >> groups shall I use to control the temperature? > > What protocol is used in published studies similar to what you're doing? > Small > groups will have larger fluctuations in temperature, that's a given. I don't > do > CG simulations, so I don't know how such groups are commonly treated. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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. -- 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.
