AMBER Archive (2008)

Subject: Re: AMBER: difference between sander and NAB

From: David A. Case (
Date: Thu Jul 10 2008 - 17:22:49 CDT

On Thu, Jul 10, 2008, Hu, Shaowen (JSC-SK)[USRA] wrote:

> Some time ago I reported a difference of MD simulation with GBSA between
> sander and NAB, which I did not take serious since I was busy on other
> staffs. Now this issue bother me since I am using NAB a lot. I think the
> non-polar part of the energy by NAB may have a problem.

Version 1.0 of AmberTools had an incorrect default value for surften, the
surface tension parameter. So you need to override the default value by
explicitly setting surften=0.005 in your NAB input file.

The AmberTools1.0 version has a test (xfin_test) which tests the nonpolar part
of NAB vs the nonpolar part of sander. So please be sure that test passes,
and take a look at its input.

This problem will be fixed in version 1.1, which is due out very soon.


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