<div> </div><div> </div><div> </div><br>Hi Justin,<br><br><pre>.mdp and fourierspacing are at below, can you tell me where is not wrong?</pre><br><br><br>; NEIGHBORSEARCHING PARAMETERS<br>; nblist update frequency<br>nstlist = 5<br>; ns algorithm (simple or grid)<br>ns_type = grid<br>; Periodic boundary conditions: xyz (default), no (vacuum)<br>; or full (infinite systems only)<br>pbc = xyz<br>; nblist cut-off <br>rlist = 0.9<br>domain-decomposition = no<br><br
>; OPTIONS FOR ELECTROSTATICS AND VDW<br>; Method for doing electrostatics<br>coulombtype = PME<br>rcoulomb-switch = 0<br>rcoulomb = 0.9<br>; Dielectric constant (DC) for cut-off or DC of reaction field<br>epsilon-r = 1<br>; Method for doing Van der Waals<br>vdw-type = Cut-off<br>; cut-off lengths <br>rvdw-switch = 0<br>rvdw = 1.2<br>; App
ly long range dispersion corrections for Energy and Pressure<br>DispCorr = EnerPres<br>; Extension of the potential lookup tables beyond the cut-off<br>table-extension = 1<br>; Spacing for the PME/PPPM FFT grid<br>fourierspacing = 0.12<br>; FFT grid size, when a value is 0 fourierspacing will be used<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>; EWALD/PME/PPPM parameters<br>pme_order = 4<br>ewald_rtol &n
bsp; = 1e-05<br>ewald_geometry = 3d<br>epsilon_surface = 0<br>optimize_fft = no<br><br>; GENERALIZED BORN ELECTROSTATICS<br>; Algorithm for calculating Born radii<br>gb_algorithm = Still<br>; Frequency of calculating the Born radii inside rlist<br>nstgbradii = 1<br>; Cutoff for Born radii calculation; the contribution from atoms<br>; between rlist and rgbradii is updated every nstlist steps<br>rgbradii = 2<br>; Salt concentration in M for Generalized Born models<br>gb_saltconc &nbs
p; = 0<br><br>; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)<br>implicit_solvent = No<br><br>; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>; Temperature coupling <br>Tcoupl = v-rescale<br>; Groups to couple separately<br>tc-grps = System<br>; Time constant (ps) and reference temperature (K)<br>tau_t = 0.1<br>ref_t = 300<br>; Pressure coupling <br>Pcoupl &
nbsp; = no<br>Pcoupltype = isotropic<br>; Time constant (ps), compressibility (1/bar) and reference P (bar)<br>tau_p = 1<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Random seed for Andersen thermostat<br>andersen_seed = 815131<br><br>; SIMULATED ANNEALING <br>; Type of annealing for each temperature group (no/single/periodic)<br>annealing = no<br>; Number of time points to use for specify
ing annealing in each group<br>annealing_npoints = <br>; List of times at the annealing points for each group<br>annealing_time = <br>; Temp. at each annealing point, for each group.<br>annealing_temp = <br><br>; GENERATE VELOCITIES FOR STARTUP RUN<br>gen_vel = yes<br>gen_temp = 300<br>gen_seed = 1993<br><br><br><br><br><br><br><div></div><br><pre><br>>Message: 4
>Date: Tue, 25 Jan 2011 08:05:44 -0500
>From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>
>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 <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>
>Message-ID: <<a href="mailto:4D3ECAA8.60807@vt.edu">4D3ECAA8.60807@vt.edu</a>>
>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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