On 7/27/13 11:48 AM, xiao wrote:
Dear Gromacs users,
I am developing the force field parameters of an organic molecule. I need to
calculate the MM energy of the molecule in a fixed conformation. For example,
in order to get the force constant of a bond, i need to calculate the energy of
the bond in different distance by using MM method and the QM method. Firstly, i
plan to scan the bond of interest up to 0.1 angstrom from the equilibrium value
at a step size of 0.005 angstrom while optimizing the structure at each step by
using QM method. Secondly, i calculate the potential energy of each structure
obtained in the previous QM optimizaiton step. Thirdly, i will calculate the
energy difference between QM and MM calculation, and finally fit the force
constant of the bond using the energy difference between QM and MM energy. My
question is that how i calculate the potential energy of each structure
obtained in QM step? I think i can get an potential energy in energy minization
step by using grompp method, but i am not sure whe!
the
r it is the energy i needed. Any advice is appreciated.
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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