From: snoze pa (snoze.pa_at_gmail.com)
Date: Thu Feb 16 2006 - 10:59:46 CST
Dear NAMD Users,
Anybody has any indea why my water box size is increasing in one direction
and decreasing in other direction when I am doing free MD run.
Here are the fig after minimization run
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/att-3398/namdmin.png
and figure after 1ns run
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/att-3398/namd1ns.png
I try to repeat simulation using useflexiblecell no, still problem remains
same.
thanks in advance
snoze
On 2/15/06, snoze pa <snoze.pa_at_gmail.com> wrote:
>
> Hi Michel, any luck with MD simulation
>
> On 2/15/06, L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu> wrote:
> >
> > snoze, could you send us the file containing your MD script, please??
> >
> > 2006/2/15, snoze pa < snoze.pa_at_gmail.com>:
> > > Dear NAMD community,
> > > I repeat my simulation in NPT. My simulation is going fine till
> > heating.
> > > However for Free MD simulation the water box size is increasing in +/-
> > Z
> > > direction, i mean in one direction while the postion of the protein
> > remain
> > > same. I don't know what is wrong with this? any solution for this
> > problem
> > > why water boz size is increading in one direction
> > > thanks in advance
> > > snoze
> > >
> >
>
>
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