Re: Fwd: Water Box size

From: snoze pa (snoze.pa_at_gmail.com)
Date: Fri Feb 10 2006 - 13:49:07 CST

Dear Phil and Ma,
I am using default value for useFlexibleCell, which i assume to be no. As
can be seen from the manual.
http://biowulf.nih.gov/apps/namd/namd-ug/node30.html

>you probably have plotted the
>positions without conversions to within the periodic box. also, the
>size of the periodic box should change in order to maintain P and T.

Shall I assume that this has nothing to do with actual dynamics of the
molecule. Or I need to change some parameter like margin etc.
thanks in advance
snoze

On 2/10/06, Philip Blood <philb_at_hec.utah.edu> wrote:
>
> Are you doing anisotropic pressure coupling (useFlexibleCell set to
> yes)? This may result in these kinds of changes in box dimensions. For
> a water box you should have the pressure control coupled in each
> direction (useFlexibleCell set to "no").
>
> Phil
>
>
> snoze pa wrote:
>
> > Dear NAMD community,
> > I am doing my simulatin at NPT. My simulation is going fine till
> > heating. ut for Free MD simulation My water box size is increasing in
> > one direction. While the postion of the protein remain same. I don't
> > know what is wrong with this? I am also attaching after 1ns simulation
> > protein and waterbox snapshot.Here are two snapshot
> > 1. namdmin.png for after minimization
> > 2. namd1ns.png is after 1ns free run.
> > I don't know why my water box size is increasing in one direction.
> > thanks in advance
> > snoze
> >
> >
> > ------------------------------------------------------------------------
> >
> >
> > ------------------------------------------------------------------------
> >
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:19:15 CST