From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Feb 16 2006 - 12:23:23 CST
Hi snoze
I suggest you to check some of the tutorials of namd. There is a good
one, that you can find here:
just change some parameters according to your simulation. I hope that
after using it, your problem will be solved.
Good luck!
Michel
2006/2/16, snoze pa <snoze.pa_at_gmail.com>:
>
> 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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