AMBER Archive (2003)

Subject: Re: saving trajectory of solute only

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Jun 09 2003 - 11:06:01 CDT

If I am not interested in water positions,
I use ptraj to strip water out of the trajectory
before viewing. I still save water coordinates
because I never know in advance if I will want
them and if not saved, it is hard to rerun the
whole simulation in explicit solvent.
carlos

----- Original Message -----
From: "Peter Anderson" <toutvabien78_at_yahoo.com>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Monday, June 09, 2003 12:01 PM
Subject: saving trajectory of solute only

> Dear Amber Users,
>
> If you're performing a molecular dynamics simulation
> of a solvated molecule, is it possible to save the
> trajectory coordinates of just the solute? If not,
> can anyone suggest how visualizing the solute molecule
> alone during the animation can be facilitated, given
> the large screen space taken by the thousands of
> solvent molecules (I use Visual Molecular Dynamics to
> do my animations)?
>
> Thank you very much,
> Peter Anderson
>
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