From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Thu Jul 23 2009 - 15:13:03 CDT
Hi,
When there is no need to use Rigidbonds all with a 1 fs, "can" we use it? Just to decrease the computer cost and the simulation time.
Thanks
Rabab Toubar
--- On Sat, 10/11/08, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
From: JC Gumbart <gumbart_at_ks.uiuc.edu>
Subject: RE: namd-l: PMEGridSize
To: rtoubar_at_yahoo.com, char_at_ks.uiuc.edu
Cc: namd-l_at_ks.uiuc.edu
Date: Saturday, October 11, 2008, 2:01 AM
8.0 cutoff 12.0 pairlistdist 13.5 margin 0.0 stepspercycle 20 rigidBonds all rigidTolerance
0.00001 rigidIterations 100 # this block specifies the Ewald electrostatics......................PME on PMETolerance 0.000001 PMEGridSizeX 32 PMEGridSizeY 32 PMEGridSizeZ 32 #block specifying the parameters for integrator and MTStimestep
1.0 fullElectFrequency 4 # this block specifies the output....outputenergies 1000 outputtiming 1000 binaryoutput no outputname output/dfn_equil restartname
output/dfni_equil restartfreq 10000 binaryrestart yes DCDfile output/dfn_equil.dcd dcdfreq 1000 #MD protocol block ...................seed 1551 numsteps 4000000 temperature 300 rescaleFreq 1 rescaleTemp 300 # this block defines periodic boundary conditions......cellBasisVector1 37.0 0.0 0.0 cellBasisVector2 0.0 31.0 0.0 cellBasisVector3 0.0 0.0 30.3 cellOrigin 0.0 00.0 0.0 wrapWater
on
of your namd.conf script:
-----------------------------------------------------------------------------------------
set temperature 310
set minimize_steps 300
set run_steps 10000000
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize $minimize_steps
reinitvels $temperature
for {set i 25} {$i < $temperature} {incr i 25} {
set tempr $i
langevinTemp $tempr
reinitvels $tempr
run 100
}
firsttimestep 0
langevinTemp $temperature
run $run_steps
On Thu, Oct 2, 2008 at 2:55 PM, Rabab Toubar <rtoubar_at_yahoo.com> wrote:
> Hi,
>
> In the namd tutorial it says on page 24: " Typically, a grid
size
> slightly less than 1 is a good
> A
> choice to reproduce charge distribution in biological systems,
> where the closest atoms have a bond separation on the order of 1
> A. Furthermore, for speed in computing Fast Fourier Transforms,
> PMEGridSizeX should be chosen so that it can be factorized by
> 2, 3, or 5. If your cellBasisVector1 = (60, 0, 0), a good
> choice for PMEGridSizeX might be 64, since 60 A/ 64 = 0.9375
> A and 64 = 26."
>
> While in the namd tutorial they used gridsizes of 32 in each direction
when
> the cellBasisVector was 42, 44 and 47, yet the simulation went OK.
>
> I am asking this as I was running a simulation of cellBasisVector around
35
> in each direction, and the gridsizes were set to 32s according to the
> tutorial. I have been looking for the reasons of the unexpected
termination
> of the simulation. And according to the tutorial this couldn't be one.
>
> * My question is, how far could the PMEGridSizes affect the simulation?
> * And if the equilibration step wasn't long enough, could this
terminate the
> simulation before completion?
>
> Thanks
> Rabab
>
>
-- Roman Petrenko. Physics Department University of Cincinnati
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