[AMBER] water cap simulation

From: Yi An <anyiphysics.gmail.com>
Date: Fri, 27 Apr 2012 16:08:03 -0500

Hi amber users,

I'm trying to simulate a protein in a water cap. My problem is during the
equilibration and simulation stages, water molecules come out of the cap so
the simulation stops. Looks like I have to use non-periodic boundary water
caps and I can't use constant pressure ensembles. Is this the reason why
waters drift out? Thanks.

Yi An
Graduate Student
Chemistry Department
Texas A&M University
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Received on Fri Apr 27 2012 - 14:30:02 PDT
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