On 8/9/13 10:33 AM, Golshan Hejazi wrote:
Hello,
Thanks for the reply. I made another even more simple test. I just would like
to understand what is going on inside the energy calculation. I have an ALA
system. This is the topology file for the bond:
[ bonds ]
; ai aj funct r k
1 2 1 1.0100e-01 3.6317e+05
3 4 1 1.0900e-01 2.8451e+05
5 6 1 1.0900e-01 2.8451e+05
5 7 1 1.0900e-01 2.8451e+05
5 8 1 1.0900e-01 2.8451e+05
1 3 1 1.4490e-01 2.8200e+05
3 5 1 1.5260e-01 2.5941e+05
3 9 1 1.5220e-01 2.6527e+05
9 10 1 1.2290e-01 4.7698e+05
From here, I computed manually the bond energy which is : sum (ki*(r_i*r_i)) =
42536.87 (kj/mol)
however, when I perform a rerun on the gro file ... this is the bond energy:
2.20074e-01 (kj/mol)
What am I missing?
It looks like you're calculating the bonded energy wrong. The energy is
calculated from the distance the bond length is from the equilibrium value, not
the bond length itself. See the manual for the necessary equation.
-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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