Hi Justin Here is the .mdp file with position restraints, which I downloaded from the martini tutorial website. It works well with the tutorial and my small triple helix, and the grompp process does not give any warnings. Please help to have a look. Many thanks to you.
define = -DPOSRES integrator = md dt = 0.02 nsteps = 50000 nstxout = 0 nstvout = 0 nstlog = 1000 nstxtcout = 1000 xtc-precision = 10 cutoff-scheme =verlet coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.9 rcoulomb = 1.4 epsilon_r = 15 vdw-modifier = force-switch rvdw-switch = 0.9 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein W tau-t = 1.0 1.0 ref-t = 310 310 compressibility = 3e-4 ref-p = 1.0 refcoord_scaling = all pbc = xyz -----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: Friday, 15 May 2015 11:50 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/14/15 9:47 PM, Ming Tang wrote: > Dear Justin, > > I saw it in the terminal. > > Potential Energy = -6.3682131e+05 > Maximum force = 1.8876091e+02 on atom 1147 > Norm of force = 3.1155257e+00 > > But, how can I further minimize my protein? > Minimization is not your problem. Post a full .mdp file of the run that is failing. -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.