[gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97
Justin A. Lemkul
jalemkul at vt.edu
Wed Jan 26 03:26:26 CET 2011
gromacs wrote:
>
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> 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
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> ; 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
>
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>>Message: 4
>>Date: Tue, 25 Jan 2011 08:05:44 -0500
>>From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at 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 at gromacs.org <mailto:gmx-users at gromacs.org>>
>>Message-ID: <4D3ECAA8.60807 at vt.edu <mailto:4D3ECAA8.60807 at 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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--
========================================
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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