On 10/3/16 2:38 AM, ISHRAT JAHAN wrote:
Dear all I am trying to simulate 3M urea in a water box.when i do the mdrun of pr , i get too many LINCS warning and also segmentation fault(core dumped). I am pasting my em.mdp and pr.mdp file below- em.mdp ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = all-bonds integrator = steep nsteps = 2000 ; ; Energy minimizing stuff ; emtol = 100 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 0.15 coulombtype = PME rcoulomb = 0.15 rvdw = .19
These cutoffs are completely nonsensical.
fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = no Pcoupl = no gen_vel = no pr.mdp ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp define = -DPOSRES
What is the purpose of position restraints here? You probably don't need any.
constraints = all-bonds constraintalgorithm = LINCS integrator = md dt = 0.001 ; ps ! nsteps = 10000 ; total 50 ps. nstcomm = 10 nstxout = 500 nstvout = 1000 nstfout = 10 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 2 coulombtype = PME rcoulomb = 2 rvdw = 2
What force field uses 2-nm cutoffs? Proper use of the force field is a prerequisite for a sensible simulation.
-Justin
fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = URE Water tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = URE Water ; Pressure coupling is on Pcoupl = Berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 thanks in advance
-- ================================================== 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.
