Water Hole

From: Jacob Poehlsgaard (mail_lists_at_hardcoil.net)
Date: Tue Sep 19 2006 - 03:00:54 CDT

Hi NAMD users

 I'm posting in this old topic because I've also run into this problem now.
I think I pretty much understand the concept of what Marcos is saying, but I
don't quite get how to implement it correctly.

 I have a RNA/protein system in a water box. I ran a lot of equilibrium runs
with constant temperature (using langvin), with gradually smaller restraints
on the various atoms to eqilibrate them and everything went well. When I
then wanted to do an actual production run (this is the first time I have
ever tried this "for real"), I switched the temperature control off. I did
this because I've read that production runs should run int the NVE ensemble,
using no environmental controls at all. In this run, a huge water hole
appeared rather rapidly.

 Should I have been using constant pressure control during my equilibrium
runs and then switched if off for production runs? If so should I switch off
both temperature and pressure controls at the same time?
 If pressure control works by rescaling the box, should I somehow alter the
cell basis vectors to fit these new dimensions in subsequent runs with the
output files?

Jacob Poehlsgaad
SDU, Denmark

> Running each part independently won't fix anything. The holes
> appear because your system is not at the appropriate density
> and you are not using constant pressure. Just turn on the
> constant pressure control (either Nose-Hoover Langevin Piston
> or Berendsen, look at the NAMD user's guide and NAMD tutorial
> for more details in www.ks.uiuc.edu) for at least 100 ps or
> more. The size of your box will eventually shrink and the
> holes will disappear once the right density is reached.
>
> Marcos
>
>
> On Sun, 21 Apr 2002, Sting wrote:
>
> > Thanks snoze pa! I'll try it.
> >
> > --Sting
> >
> > =================================
> >
> > try to run each part seperately.
> > 1. minimization.
> > 2. equlib.
> > 3. free md
> > goodluck
> >
> >
> > On 4/19/02, Sting <stg1979_at_emails.bjut.edu.cn> wrote:
> > Dear All,
> >
> > I am using namd to study trihelices in the water box.
> Minimization and
> 500ps CA restrained dynamics were performed. I found a strange
> phenomenon: sevral holes without water formed in the water
> box(even afer
> adding the water layer to 15 angstrom),and with the rotating of the
> trihelices,the holes seem moving accordingly. Still when performing
> SMD,the water holes remain and adjust while going on. I
> wondered how to
> explain it and how to tackle the problem. Could anyone
> offer some help?
> Thanks.

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