AMBER Archive (2006)

Subject: Re: AMBER: hessian calculation

From: sebnem (sebnem_at_mercury.chem.pitt.edu)
Date: Thu Mar 30 2006 - 10:22:23 CST

David A. Case wrote:

>On Wed, Mar 29, 2006, sebnem_at_mercury.chem.pitt.edu wrote:
>
>
>
>>I think when i use icons option in nmode, in the second derivative
>>calculation part, it uses the restraints on the whole molecule not only
>>on the group that I define in the input file.
>>
>>
>
>
>Take a look at xconst.f: it does look like the diagonal second derivatives
>are all modified, independent of the value of wref.
>
>You could try this code (Untested!):
>
> if (ndrv == 2) then
> k = 0
> do 20 i=1,nr
> k = k + i
> dd(k) = dd(k) + wref(((i-1)/3)+1)
> 20 continue
> end if
>
>I will poke around and see what I can find. I'm sure that this stuff is
>almost never used, since the physical meaning of modes with constraints
>is itself problematic.
>
>...thanks for the report...dac
>
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>
thanks a lot. I think this will solve my problem.
sebnem

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