On Sun, Aug 7, 2011 at 10:50 AM, Anglea A. <a.anglea90.yahoo.com> wrote:
> Dear all
> I have been asked to add one more term in the EAM1,SCF during the
> simulation. The added term is a simple equation that should be considered
> during EQM calculation.
> I don't know where can I find the Energy equation for QMMM simulation,
> which file?.
>
This depends largely on what term you want to add, and how it's supposed to
be added. If it can be added after the QM calculation is done, then just
look in the sander source code (the force() routine is the main driver for
all of the energies and forces). If it is a new term/perturbation or
something in the quantum hamiltonian, then you will have to modify the
appropriate function in $AMBERHOME/AmberTools/src/sqm.
Is there any other point should be considered in case of change
> the original equation (rather than definition of the new implemented
> parameters).
>
Yes. Do you plan on doing any kind of dynamics with this additional term?
If so, you'll need the first derivative of this term, and you'll need to add
its contribution to the force appropriately. If not, you won't be sampling
from your desired ensemble.
HTH,
Jason
> Cheers
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Aug 07 2011 - 20:00:02 PDT
