Hi I am having some pressure coupling issues. I have a fairly large protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I run NVE it conserves energy with appropriate parameter settings. If I run NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello Rahman), the system just continuously expands. My parameters are as follows. Any ideas?
Best, Ilya ; ; File 'mdout.mdp' was generated ; By user: relly (508) ; On host: master.simprota.com ; At date: Fri Mar 6 20:17:33 2009 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.004 ;nsteps = 250000 nsteps = 2500000 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step = 0 ; mode for center of mass motion removal comm_mode = linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm_grps = system ; 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 = 10 nstenergy = 10 ; Output frequency and precision for xtc file nstxtcout = 250 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 = protein ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist = 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = .9 rcoulomb = 1.0 ; Relative dielectric constant for the medium and the reaction field epsilon-r = 80 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = .9 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; 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 = 1.e-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 = 298.0 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 10 compressibility = 4.5e-5 ref_p = 1.01325 ; Scaling of reference coordinates, No, All or COM refcoord_scaling = No ; Random seed for Andersen thermostat andersen_seed = 815131
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