AMBER Archive (2004)

Subject: AMBER: Octahedron Box

From: Seonah Kim (kim_at_qtp.ufl.edu)
Date: Mon Jun 28 2004 - 10:30:34 CDT


Dear All,

I have a question about the explicit water model.
I am using Trpcage with water model using Amber 8.
When I run the VMD after MD, Trpcage is jumping around the water box. Sometimes
protein is in the middle of box but sometimes is at the edge of the box. Can I
put the protein inside of the box only?

Thank you for your help in advance.

Seonah Kim

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