AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Jul 13 2006 - 14:00:59 CDT

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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