Re: regarding simulation

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue May 05 2009 - 10:22:25 CDT

Prasun,
the dielectric constant that you set in the config file is applied to
all electrostatic interactions. If you have tip3p water in the system
then there is no need to also have a background dielectric; the water
itself acts as the dielectric medium!

I will send you a config file off-list to avoid spamming everyone with
large text attachments.
Peter

prasun kumar wrote:
> thanx alot for the reply. i have solvated my system in TIP3P which is
> havin dielectric constant of 82. Now the volume has exceeded the
> highest value and giving 999999999s ome thing like this. what should I
> do. can you please send me one of your configuration file used for
> simulation.....
> waiting for the positive reply
> with regards
>
> PRASUN (ASHOKA)
>
>
> On Tue, May 5, 2009 at 8:46 PM, Peter Freddolino <petefred_at_ks.uiuc.edu
> <mailto:petefred_at_ks.uiuc.edu>> wrote:
>
> It's probably because you're using a very short cutoff, no long range
> electrostatics, and a high dielectric with a (presumably) solvated
> system.
> Peter
>
> prasun kumar wrote:
> > respected all
> >
> > I have just now started simulation using NAMD
> > for MD I am using *numsteps *parameter in place of *minimize* that i
> > have used while doing minimization. till minimization its working
> fine.
> > actually I want to check the interaction between two proteins for
> that I
> > need to do the simulation. Now the problem I am facing is following:
> >
> > Energy of the system is increasing continuosly and the volume is also
> > increasing.
> > I am attaching my configuration file also.
> > The problem I am facing is it because of the fact that I m not
> using NVT
> > during my simulation or some thing else. I am getting the same result
> > when I am replacing *numsteps *by *run*.
> >
> > lookin forward for your positive reply
> >
> > with regards
> >
> > PRASUN (ASHOKA)
> >
>
>

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