Hi Chris, When I create the topology for the 4fs timestep I use pdb2gmx -vsite h. I set up the correct constraints. I've tested it and it conserves energy in NVE. I run all he sims with constraints=all-bonds. I am now running a single water box (800 water molecules) with 1s time steps and the volume keeps blowing up.
Thanks, Ilya On Wed, Apr 8, 2009 at 8:37 AM, <chris.ne...@utoronto.ca> wrote: > Hi Ilya, > > If you did include the entire mdp file then you have a time step of 4 fs > and no constraints (other than water). For a timestep of 2 fs, you should > constrain all-bonds (or some would say at least h-bonds) and for 4 fs then > you should also constrain angles involving hydrogens (need a new .itp file > for this). > > Can you try with a 1 fs timestep and see how it goes? Still, I am surprised > that everything works out at NVT, but this is certainly worth the test. > > Do you have other systems running fine with these mdp options in NVT? > > Chris. > > -- original message -- > > HI Chris, > > On Tue, Apr 7, 2009 at 9:31 PM, <chris.neale at 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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