AMBER Archive (2003)

Subject: Isotropic Solvent Box

From: N. Jiten Singh (jiten_at_postech.ac.kr)
Date: Thu Feb 13 2003 - 05:28:55 CST

Dear Amber Users,

When I generate the solvent Box using SolvateBox with iso options it is shown to create the cubic box -but when I save it using saveoff the boundbox parameters have ractangular box parameters. Then I modify the box parameters to be cubic in Topology file after saving top anc crd files. When I equilibrated the solvent box using Sander or Sander_classic it forms ractangular equlibrated box.

I am interested in making a perfect equlibrated box just like it is provided in Amber solvents.lib.

Can anyone help me to create an equlibrated cubic Box.

Thanking you,

Best wihses

N. Jiten Singh
Center for Superfunctional Materials
Department of Chemistry
Pohang University of Science and Technology
San 31, Hyojadong, Namgu
Pohang 790-784, Korea
Phone : 82-54-279-5853 ( Lab )
Fax : 82-54-279-8137 (or +82-54-279-3399)
Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e