On 6/22/17 9:21 AM, Sergio Manzetti wrote:
Justin, I fixed the sim.mdp, however I realized I sent you the wrong mdp file, the one that gave DNA minimization problem is the EM.mdp Which is this: define = integrator = steep emtol = 100.0 emstep = 0.001 nsteps = 100000 ; output frequency nstxout = 50 nstvout = 0 nstfout = 0 nstlog = 50 nstenergy = 50 nstxtcout = 0 xtc_grps = system ; nstlist = 10 pbc = xyz rlist = 0.8 cutoff-scheme = group coulombtype = PME rcoulomb = 0.8 vdwtype = cut-off rvdw = 0.8 DispCorr = EnerPres ; constraints = none constraint_algorithm = LINCS implicit_solvent = no E_x = E_y = E_z = However, it looks completely normal... Still the system is not apprently equilibrated 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors
Follow the link I provided before about diagnosing the problem. -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.
