[gmx-users] Fw:Re:gmx-users Digest, Vol 81, Issue 192; PME, Estimate for the relative

[gromacs]

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" <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>
>Message-ID: <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
>
>========================================
>
>
>------------------------------
>



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110126/f5164597/attachment.html>