Thanks, Justin For a stable system, is it true that it can be equilibrated endlessly without error? I got LINCS errors when my protein had been equilibrated for about 50ns. Does this mean that there is some wrong with my system?
-----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Saturday, 23 May 2015 6:24 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] first residue in chains warning issue On 5/22/15 3:39 AM, Ming Tang wrote: > > Dear Justin, > > Is there any significant difference between the equilibrated states of the > protein equilibrated by NPT with all-bonds constrained and without any > constraints? > If the difference is quite small, then I can choose constraining bonds to > increase time step. > This is generally (read: pretty much always) what people do in biomolecular simulations. The bonds are rarely (read: practically never) excited from their ground state, so constraints are a reasonable approximation. This isn't universal, but it's definitely true in most biological systems at ambient conditions. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
