On Wed, Apr 8, 2009 at 7:53 AM, Joe Joe <ilcho...@gmail.com> wrote: > 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. >
It is indeed supported and does work correctly. But you have to set coulombtype PME-Switch. mdp options says: "This is mainly useful constant energy simulations. For constant temperature simulations the advantage of improved energy conservation is usually outweighed by the small loss in accuracy of the electrostatics. " Roland > >> >> 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. Use thewww interface >> or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > _______________________________________________ > 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. 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 > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
_______________________________________________ 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. 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