Thank you very much.
Shaowen
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of David A. Case
Sent: Thursday, July 10, 2008 5:23 PM
To: amber.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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Received on Sun Jul 13 2008 - 06:07:47 PDT
