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

From: David A. Case <case.scripps.edu>
Date: Thu, 18 Aug 2005 07:39:55 -0700

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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Received on Thu Aug 18 2005 - 15:53:01 PDT
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