AMBER Archive (2005)

Subject: AMBER: Density of Cyclohexane box

From: chaiann ng (andy810915_at_hotmail.com)
Date: Wed Nov 02 2005 - 21:57:49 CST

Dear Amber User,

I am trying to create a cyclohexane box for my simulation. I am using the
input for under the folder "solvent" in the amber directory and also the
input file from the web. I am getting density of less than 0.4 at 300K after
50ps MD, which is the initial density when i solvate my cyclohexane (chair
conformation) with a box of cyclohexane. Can anyone help? Attached is the
PDB file of the cyclohexane and prepin file. Thanks.

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