HI Chris, On Tue, Apr 7, 2009 at 9:31 PM, <chris.ne...@utoronto.ca> wrote:
> Hi Ilya, > > First thing that comes to mind is that it is strange to couple a coulombic > switching function with PME. While this could possibly be done correctly, I > doubt that it is in fact done in the way that you expect (i.e. correctly) in > gromacs. In fact, I think that grompp/mdrun should probably throw an error > here -- unless it is actually handled in the proper way, and a developer > could help you here to figure out if you are indeed getting what you desire. > > coulombtype = PME > rcoulomb-switch = .9 > rcoulomb = 1.0 I am pretty sure gromacs ignores the rcoulomb-switch parameter in the case of PME but I will give it a try. > > > However, it is not clear to me that this should cause a system to > "continuously expand". > > Still, you do not give very good information about what you mean by > "continuously expand". Can you please provide some information on that? e.g. > amount of time and total volume change. My box density goes from ~1.0 to .5 in 5 ps with a compressibility of 5E-05. It goes from ~1.0 to .94 in 300 ps with a compressibility of 5E-06. In both case the slope of density(t) is negative and never levels off. > > Chris > > -- original message -- > > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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. 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