[gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97
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? 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 Is my setting proper? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97
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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97
On 26/01/2011 12:05 AM, Justin A. Lemkul wrote: 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 ... and the relevant manual sections. Mark 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97
gromacs wrote: Hi Justin, .mdp and fourierspacing are at below, can you tell me where is not wrong? I see nothing wrong with the .mdp file, per se, although it does not appear complete (no integrator, nsteps, etc). Perhaps that was your intention, but if nsteps is left at default (0), then you shouldn't worry about poor performance :) The amount of time spent doing PME calculations depends on what is in your system. While your settings seems reasonable in a generic sense, if you have a large, highly-charged system, then much of the work will be allocated to PME. In that case, you may have to re-think how you balance the real space and reciprocal space terms. This involves possibly increasing (slightly) the values of rcoulomb and fourierspacing, if and only if the PME load is prohibitive and you are sure you won't incur any unnecessary error. g_pme_error may help there. -Justin ; 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 ; App ly 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 n bsp; = 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 nbs p;= 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 nbsp;= 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 specify ing 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 mailto:jalem...@vt.edu Subject: Re: [gmx-users] V-rescale thermostat, PME, Estimate for the relativecomputational load of the PME mesh part: 0.97 To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4d3ecaa8.60...@vt.edu mailto: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
