Re: PBC without solvent

From: David A. Case <>
Date: Tue, 18 Mar 2003 07:38:04 -0800

On Tue, Mar 18, 2003, Franck Chevalier wrote:

> I have a new question about using Periodic boundary condition in AMBER
> 6.0. Is it possible to run PBC dynamics without including solvent in my
> input files (.crd and .top)? I would like first to equilibrate my system
> with PBC before adding the solvent (water). I read that the dimensions
> of the box have to be written in the .crd and .top files.

I don't understand why you want to do this. How big is your box? Do
you expect solute molecules in different cells to interact with one another?
(Amber is not set up to handle calculations of that sort). What is wrong
with the two "standard" options (equilibrating in vacuum, then adding water;
add water, then equilibrating the whole system)?


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Tue Mar 18 2003 - 15:53:01 PST
Custom Search