Yeah I only gave a partial. Tried to remove the QM params. I do use constraints = all-bonds.
On Wed, Apr 8, 2009 at 9:18 AM, <chris.ne...@utoronto.ca> wrote: > You say "I run all he sims with constraints=all-bonds", but I don't see > that in the mdp options that you provided. I even put your text in a file > and grepped for it just to be sure. Did you only give us a partial mdp file? > > Try adding this to your mdp file: > > constraints = all-bonds ; REMOVE_FOR_EM > constraint_algorithm= lincs ; REMOVE_FOR_EM > lincs-iter = 1 ; REMOVE_FOR_EM > lincs-order = 6 ; REMOVE_FOR_EM > > see, for example, > http://www.gromacs.org/pipermail/gmx-users/2008-October/037545.html > http://www.gromacs.org/pipermail/gmx-users/2008-November/037673.html > > --- original message --- > > > 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.neale at 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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