On 10/1/15 9:07 AM, badamkhatan togoldor wrote:
Dear Gromacs Users,I would like to use g_membed to insert my peptide into membrane. But I got this errors and notes in grompp ERROR 1 [file membed.mdp]: Energy group exclusions are not (yet) implemented for the Verlet scheme NOTE 4 [file membed.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 5 [file membed.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics.membed.mdp file include following options: integrator = md energygrps = Protein freezegrps = protein freezedim = Y Y Y energygrp_excl = protein protein nsteps = 1000 So I don't know I have to put more options? or use other .mdp file? If someone have appropriate .mdp file, please share !
The error and note 4 are related to the Verlet scheme, so switching to "cutoff-scheme = group" is needed here. For note 5, it's probably not that big a deal in this context, but don't try to run a simulation with a plain cutoff.
-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.
