Hi Justin,
.mdp and fourierspacing are at below, can you tell me where is not wrong? ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; 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 = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = 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 = 300 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 ; Random seed for Andersen thermostat andersen_seed = 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = no ; Number of time points to use for specifying annealing in each group annealing_npoints = ; List of times at the annealing points for each group annealing_time = ; Temp. at each annealing point, for each group. annealing_temp = ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 300 gen_seed = 1993 >Message: 4 >Date: Tue, 25 Jan 2011 08:05:44 -0500 >From: "Justin A. Lemkul" <jalem...@vt.edu> >Subject: Re: [gmx-users] V-rescale thermostat, PME, Estimate for the > relative computational load of the PME mesh part: 0.97 >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <4d3ecaa8.60...@vt.edu> >Content-Type: text/plain; charset=UTF-8; format=flowed > > > >gromacs wrote: >> HI Friends, >> >> I get the following note, >> >> The Berendsen thermostat does not generate the correct kinetic energy >> distribution. You might want to consider using the V-rescale thermostat. >> >> I want to keep the T at 300K, so does it matter to select any thermostat >> method? >> > >The choice of thermostat certainly does matter, otherwise you wouldn't get >this >note. Refer to the numerous discussions in the list archive as to why one >would >or would not (usually) use the Berendsen thermostat, as well as: > >http://www.gromacs.org/Documentation/Terminology/Thermostats >http://www.gromacs.org/Documentation/Terminology/Berendsen > >> >> Another note when i use PME: >> >> Estimate for the relative computational load of the PME mesh part: 0.97 >> >> NOTE 1 [file aminoacids.dat, line 1]: >> The optimal PME mesh load for parallel simulations is below 0.5 >> and for highly parallel simulations between 0.25 and 0.33, >> for higher performance, increase the cut-off and the PME grid spacing >> >> So what is the reason? I use type=PME >> > >Your combination of settings (rcoulomb, fourierspacing, and perhaps a few >others) indicate that your simulation is going to spend an inordinate amount >of >time doing PME calculations, so your performance will suffer. Seeing your >entire .mdp file would be necessary if you want further guidance. > >-Justin > >> Is my setting proper? >> >> Thanks >> >> > >-- >======================================== > >Justin A. Lemkul >Ph.D. Candidate >ICTAS Doctoral Scholar >MILES-IGERT Trainee >Department of Biochemistry >Virginia Tech >Blacksburg, VA >jalemkul[at]vt.edu | (540) 231-9080 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >======================================== > > >------------------------------ >
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