[AMBER] Simulation cell reduction

From: Lorenzo Gontrani <l.gontrani.caspur.it>
Date: Thu, 15 Jul 2010 12:15:47 +0200

Dear Amber users, I am facing the following problem:
I have an equilibrated simulation cell of a liquid of dimension 40X40X40
A^3, and I would like to extract a smaller cube from this box (let's
say, a small box 20X20X20 in the center), to perform a bench of tests by
varying the force field.
I tried several strategies, but all of them are "centrosymmetric" (based
on the distance), and when I try to "rebond" the atoms escaped from the
mimimum image (molecules are broken across the boundary), I get big void
in the center, and molecules still tore apart. I tried to do it with the
command "pbc join bonded" of VMD pbctools package.
Can anybody of you suggest me some way to do it?

Thanks a lot


Lorenzo Gontrani
Research associate of EDXD group
University of Rome "La Sapienza"
GSM +39 338 7615798
Email l DOT gontrani AT caspur DOT it
Webpage: http://webcaminiti/gontrani.html
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Received on Thu Jul 15 2010 - 03:30:03 PDT
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