AMBER: How to build a cubic box of a newly synthesized compound?

From: Jeffrey <>
Date: Wed, 24 Dec 2008 14:34:13 +0800

 Dear all,

      I'd like to perform a md simulation of a newly synthesized compound to calculate the dielectric constant. But before the md is carried out, a cubic box of the compound should be built with a reasonable density. But I don't know how to place the molecules in the box, such as orientation, relative position etc. Could someone please give me suggestions on how to do it conveniently?

Thanks very much for the time.
Happy Christmas day.

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Received on Wed Dec 24 2008 - 01:25:31 PST
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