AMBER Archive (2006)

Subject: Re: AMBER: hessian calculation

From: David A. Case (case_at_scripps.edu)
Date: Wed Mar 29 2006 - 18:08:34 CST

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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