Please find below =============================== integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.001 nsteps = 1000000 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps =
; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed ;bd-temp = 300 ;bd-fric = 0 ;ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 50 emstep = 0.005 ; Max number of iterations in relax_shells niter = 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 5000 nstenergy = 2500 ; Output frequency and precisiofor xtc file nstxtcout = 50 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 50 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.45 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field-zero epsilon_rf = 0 rcoulomb-switch = 0 rcoulomb = 1.3 vdw-type = Shift ; cut-off lengths rvdw-switch = 1.1 rvdw = 1.3 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = V-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.1 ref_t = 348 ; Pressure coupling Pcoupl = no ;Parrinello-Rahman Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1.0 compressibility = 4.5e-6 ref_p = 1.00 ; Random seed for Andersen thermostat andersen_seed = 815131 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no gen_temp = 298.15 gen_seed = 1993 ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are exclud energygrp_excl = ; NMR refinement stuff ; Distance restraints type: No, Simple or Ensemble disre = No ; Force weighting of pairs in one distance restraint: Conservative or Equal disre-weighting = Conservative ; Use sqrt of the time averaged times the instantaneous violation disre-mixed = no disre-fc = 1000 disre-tau = 0 ; Output frequency for pair distances to energy file nstdisreout = 100 ; Orientation restraints: No or Yes orire = no ; Orientation restraints force constant and tau for time averaging orire-fc = 0 orire-tau = 0 orire-fitgrp = ; Output frequency for trace(SD) to energy file nstorireout = 100 ; Dihedral angle restraints: No, Simple or Ensemble dihre = No dihre-fc = 1000 ; Output frequency for dihedral values to energy file =============================== On Mon, Jan 25, 2010 at 10:27 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Vitaly V. Chaban wrote: >>> >>> 1. No problem at all in vacuo? That with a 1 fs timestep and the sd >>> integrator? Strange then that your molecule is ok and the water is ok, >>> but they are unstable together. Perhaps your'e not getting any LJ >>> interactions (or not correct ones) between your solute and water? That's >>> where I would focus my efforts if I was you. I suppose it could also be >>> solute-solute LJ problems... >> >> If I switch off electrostatics between CIP and water, the problem >> disappeared... Maybe it's really worth to use a smaller timestep for >> this system ... > > Can you post your .mdp file? > -- 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/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/mailing_lists/users.php
