AMBER Archive (2006)Subject: Re: AMBER: hessian calculation
From: sebnem_at_mercury.chem.pitt.edu
Date: Tue Mar 28 2006  18:20:18 CST
I actually don't need different force constants for restraints. By chance
when i was playing with the force constant , i noticed this. After that i
become suspicious about my calculation. There should not be any
contribution of this force constant on the part of the hessian from
nonrestrained atoms.
Here is an example of two inputs that i used with same coordinate,topology
and reference coordinates for restraints.
obtain gasphase normal modes
&data
ntrun = 1, nsave=1, ndiag=2, cut=999.0, ntx=1,
nprint=1,
drms = 5, maxcyc=1,
scnb=2.0, scee=2.0,idiel=1,
nvect=1,ntx=1,ntxo=1,icons=1,
&end
group
1
RES 35 279
END
END
obtain gasphase normal modes
&data
ntrun = 1, nsave=1, ndiag=2, cut=999.0, ntx=1,
nprint=1,
drms = 5, maxcyc=1,
scnb=2.0, scee=2.0,idiel=1,
nvect=1,ntx=1,ntxo=1,icons=1,
&end
group
10
RES 35 279
END
END
For hessian calculation, i used nmode.f .Inside subroutine fillm, I put a
print statement inside the loop. I suppose the first value
that i will get from this will be a(1,1) which does not have anything to
the with the force constant on residues 35279. However i got two
different values for a(1,1) as well as some other elements.
Am I doing something wrong?
thanks again,
sebnem
On Tue, 28 Mar 2006, David A. Case wrote:
> On Tue, Mar 28, 2006, sebnem wrote:
>
> > My question is how the force constant on the restrained atoms
> > can effect the second derivative of the potential with respect to the
> > nonrestrained coordinates?
>
> It should not have such an effect. I wonder if your qualitative description
> really captures exactly what you did. Why were you changing the force
> constant for the restraining forces?
>
> ...dac
>
> 
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