On 12/27/14 11:42 AM, elham tazikeh wrote:
Dear users when i simulated Aspirin on Human serum albumin (pdb: 2i30) in equilibration process (NVT), i encountered with below message and my simulation stopped. i dont know why?
http://www.gromacs.org/Documentation/Terminology/Blowing_Up A seg fault leaves nothing to diagnose. Follow the advice in that link. -Justin
*pdfco@pdfco-X:~/Aspirin$ tail nvt.job-nex int 0 Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange.-reseed int -1 Seed for replica exchange, -1 is generate a seed-[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system* *Reading file nvt.tpr, VERSION 4.6.5 (single precision)Using 1 MPI thread[1]+ Segmentation fault (core dumped) mdrun -v -deffnm nvt &> nvt.job* my *NVT.mdp* content was: title = Protein NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 100000 ; 0.002 * 100000 = 200 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 0.2 ps nstvout = 1000 ; save velocities every 0.2 ps nstenergy = 1000 ; save energies every 0.2 ps nstlog = 1000 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = v-rescale tc-grps = Protein_SAL SOL_CL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = XYZ ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed i really appriciate for your hint regards
-- ================================================== 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.
