AMBER Archive (2008)

Subject: RE: AMBER: difference between sander and NAB

From: Hu, Shaowen (JSC-SK)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Fri Jul 11 2008 - 08:02:51 CDT


Thank you very much.

Shaowen

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Thursday, July 10, 2008 5:23 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: difference between sander and NAB

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.

...dac

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