AMBER Archive (2006)

Subject: Re: AMBER: hessian calculation

From: sebnem (sebnem_at_mercury.chem.pitt.edu)
Date: Tue Mar 28 2006 - 20:53:59 CST

just one more addition to my last e-mail,
The difference is only on the diagonal elements of hessian. There is no
problem on the off-diagonal elements.
I'll really appreciate any help,
sebnem

> 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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Sebnem Essiz

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