Tutorial-l Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Oct 03 2008 - 21:53:25 CDT

Many shortcuts are taken in the NAMD tutorial simulations in the
interest of speed; I'm not sure how much the PME grid size affects
speed though (you could check yourself if interested). Therefore,
what's written in the tutorial is much more important than what's in
the configuration files themselves. While the simulation may appear
to run fine with a coarse PME grid for a while, it's not accurate.

Regarding why your simulation terminated unexpectedly, you will need
to give us more information to determine that.

On Oct 3, 2008, at 3:22 PM, Rabab Toubar wrote:

> So you are suggesting leaving the Grid Size as (32s) is and doing
> this gradual heating?
>
> Thanks Roman,
> Rabab
>
> --- On Thu, 10/2/08, Roman Petrenko <rpetrenko_at_gmail.com> wrote:
> From: Roman Petrenko <rpetrenko_at_gmail.com>
> Subject: Re: namd-l: PMEGridSize
> To: rtoubar_at_yahoo.com
> Cc: tutorial-l_at_ks.uiuc.edu, namd-l_at_ks.uiuc.edu
> Date: Thursday, October 2, 2008, 4:22 PM
>
> gradual heating solved similar problem in my case. put this at the end
> 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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