AMBER Archive (2005)

Subject: Re: AMBER: difference of energy in sander and nmode in amber 7

From: David A. Case (case_at_scripps.edu)
Date: Thu Aug 18 2005 - 09:39:55 CDT

On Wed, Aug 17, 2005, sebnem wrote:

> Thanks a lot for your suggestion, but i need to use either ibelly or ntr
> in nmode, in order to have something consistent with sander. I need nmode
> for second derivative calculation. So i have to find a way to bring nmode
> and sander to the same place. Please help me!

The interpretation of normal mode calculations using either ntr or ibelly
options is quite tricky; be sure you know what you are really looking for
before going down this road. That said, it is probably simplest to use ntr
if you need to add constraints.

....dac

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