Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be reasonable according to gromacs website. So ijust kept trying 0.02ps
Sent from my Huawei Mobile Justin Lemkul <jalem...@vt.edu> wrote: On 5/14/15 10:02 PM, Ming Tang wrote: > 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 Have you tried simply reducing the time step? 20 fs may be reasonable for a well equilibrated system, but if the run is dying early, then this is the first thing I would look at. -Justin > 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. > -- ================================================== 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.
