AMBER Archive (2003)

Subject: Re: AMBER: water box problem

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Thu Jul 24 2003 - 06:36:29 CDT

since the system is periodic, I don't think it really
matters if your solute is toward the end or in
the middle...
Carlos

----- Original Message -----
From: "Omar Wahab" <paxomw_at_nottingham.ac.uk>
To: <amber_at_scripps.edu>
Sent: Thursday, July 24, 2003 4:32 AM
Subject: AMBER: water box problem

> Dear AMBER users,
>
> I am trying to simulate the unfolding of an RNA duplex in explicit
solvent. I want to keep the amount of waters in the system to a minimum. I
want to make a box with dimensions of approximately 40Ax40Ax100A with the
solute positioned close to one end of the box rather than the centre of the
box which Xleap produces. Is ther any way to position the solute at one end
of the box as opposed to the centre?
>
> Thanks,
> Omar Wahab
>
>
> Omar Wahab
> PhD Student=20
> Computational Modelling and Informatics Group
> School of Pharmaceutical Sciences
> University of Nottingham
> Nottingham NG7 2RD
>
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