[AMBER] autoimage and TI

From: Khabiri, Morteza <khabiri.med.umich.edu>
Date: Tue, 24 May 2016 14:44:34 +0000

Hi all

I have a system including DNA and water+ions in it with the octahedron box shape. For some reason iwrap is off and the waters and ions overflowing. In the next step, I am going to try FEP calculation on it. Before starting FEP, I am going to try warping the system by cpptraj (autoimage option) first and going to run FEP on it. So I want to be sure, would wrapping effects the coordinate or i.e thermodynamics properties of the system?

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Received on Tue May 24 2016 - 08:00:03 PDT
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