Tutorial-l Mailing List

From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Fri Oct 03 2008 - 15:22:19 CDT

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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