AMBER Archive (2006)

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

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Thu Jul 13 2006 - 14:49:39 CDT

OK. Thanks!

Gustavo.

On 7/13/06, Carlos Simmerling <carlos_at_csb.sunysb.edu> wrote:
> then I think using ptraj to center the peptide and image the water
> for each frame should be ok.
>
> Gustavo Seabra wrote:
>
> > 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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