AMBER Archive (2006)

Subject: Re: AMBER: center molecule using iwrap=1?

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Thu Jul 13 2006 - 14:07:40 CDT

Well, I want, for exemple, to locate all water molecules within some
distance from the peptide, using for example a VMD script. If the
molecule is close to the edge of the box, then the script gets more
complicated (although it's not impossible...)

Thanks,

Gustavo.

On 7/13/06, Carlos Simmerling <carlos_at_csb.sunysb.edu> wrote:
> you could use a positional restraint on one or more atoms
> to keep the peptide in the center but I would worry about the
> effect on the dynamics. I would think it would be better to let
> it drift and then use ptraj to center it, then do your analysis on
> that trajectory. it's hard to really say much more since you don't
> say why your analysis will need it centered.
>
> Gustavo Seabra wrote:
>
> > Hi All,
> >
> > I have a system of a small peptide in explicit water.
> >
> > I know that, using ptraj, I can put the peptide inthe center of the
> > box and wrap all waters around it, so as to create a new crd file with
> > my molecule always in the center of the box and wrapping the waters
> > around it.
> >
> > I wonder if something like it is possible by using iwrap=1 instead. I
> > mean, define it to wrap the molecules, (iwrap=1) AND keep the peptide
> > in the center od the box. Is that possible? How?
> >
> > (I'm worried that just with iwrap=1 alone the peptide will be allowed
> > to drift inside the box. Although it has no effect on the dynamics, it
> > will change the analysis I want to do later.)
> >
> > Thanks a lot!
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