AMBER Archive (2006)

Subject: Re: AMBER: hessian calculation

From: sebnem (sebnem_at_mercury.chem.pitt.edu)
Date: Tue Mar 28 2006 - 20:41:52 CST

Thanks a lot for your quick response.
Actually the system is not that big, I only have around 700 atoms in the
molecule.
The restrained residues are just dummy atoms. I also checked the forces on
non-restrained atoms,and different force constants on restrainted atoms
does not make any difference in the force of non-restrained atoms.
Problem is with the second derivative calculation.Is there a difference
between the implementation of ntr option in sander and icons option in
nmode?
thanks again,
sebnem

<quote who="David A. Case">
> On Tue, Mar 28, 2006, sebnem_at_mercury.chem.pitt.edu wrote:
>
>> group
>> 1
>> RES 35 279
>> END
>> END
>
> I don't see anything obviously wrong, but this is a very big system to
> be doing normal modes on. If you want to explore things in more detail,
> try printing out the Hessian elements for a very small test case, and
> work your way up in size.
>
> ...dac
>
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Sebnem Essiz

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