the same mdp file does the equlibriation fine at dt =0.0002 rather than 0.002.what could be the problem.if so can i continue using 0.0002 for dt in this simulation.Anad also the cnt is not infinite adn also the graphen sheets are not infinite.
On Sat, Jun 11, 2011 at 4:52 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > sreelakshmi ramesh wrote: > >> >> >> ---------- Forwarded message ---------- >> From: *sreelakshmi ramesh* <sree.laks...@research.iiit.ac.in <mailto: >> sree.laks...@research.iiit.ac.in>> >> Date: Sat, Jun 11, 2011 at 4:37 PM >> Subject: Re: error during equilibriation >> To: Discussion list for GROMACS users <gmx-users@gromacs.org <mailto: >> gmx-users@gromacs.org>> >> >> >> here goes my mdp file.The when i attach the top file by mail is getting >> bounced back.Thanks in adcvance >> >> >> >> title = double walled cnt between graphene sheets >> > > Is the CNT and/or the graphene infinite? If any species are, then you need > to use the periodic_molecules keyword. > > How successful was energy minimization? What was the output (Fmax and > Epot)? > > I see nothing particularly wrong with the .mdp file (other than perhaps the > keyword mentioned above), so that suggests either the topology or the > initial configuration is not sound. > > -Justin > > > define = -DPOSRES ; position restrain the protein >> ; Run parameters >> >> integrator = md ; leap-frog integrator >> nsteps = 50000 ; 2 * 50000 = 100 ps >> dt = 0.002 ; 2 fs >> ; Output control >> nstxout = 100 ; save coordinates every 0.2 ps >> nstvout = 100 ; save velocities every 0.2 ps >> >> >> nstenergy = 100 ; save energies every 0.2 ps >> nstlog = 100 ; 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 ; modified Berendsen thermostat >> tc-grps = system ; two coupling groups - more accurate >> tau_t = 0.1 ; time constant, in ps >> >> >> ref_t = 300 ; reference temperature, one for each >> group, in K >> ; Pressure coupling is off >> pcoupl = no ; no pressure coupling in NVT >> ; Periodic boundary conditions >> pbc = xyz ; 3-D PBC >> ; 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 >> >> >> >> >> here goes the error >> Not all bonded interactions have been properly assigned to the domain >> decomposition cells >> >> >> A list of missing interactions: >> Angle of 2097 missing 14 >> Ryckaert-Bell. of 1286 missing 12 >> LJ-14 of 2801 missing 8 >> exclusions of 31870 missing 14 >> >> Molecule type 'ICE' >> the first 10 missing interactions, except for exclusions: >> LJ-14 atoms 79 299 global 79 299 >> LJ-14 atoms 165 299 global 165 299 >> Angle atoms 167 207 299 global 167 207 299 >> Ryckaert-Bell. atoms 167 207 299 285 global 167 207 299 285 >> Ryckaert-Bell. atoms 173 175 285 299 global 173 175 285 299 >> LJ-14 atoms 173 299 global 173 299 >> LJ-14 atoms 173 352 global 173 352 >> Angle atoms 175 285 299 global 175 285 299 >> Angle atoms 175 285 352 global 175 285 352 >> Ryckaert-Bell. atoms 175 285 299 207 global 175 285 299 207 >> >> ------------------------------------------------------- >> Program mdrun, VERSION 4.5.3 >> Source code file: domdec_top.c, line: 356 >> >> Fatal error: >> 48 of the 46602 bonded interactions could not be calculated because some >> atoms involved moved further apart than the multi-body cut-off distance (1 >> nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and >> tabulated bonds also see option -ddcheck >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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