Hello,
Recently, I'm doing tests on AMBER Forcefield. I found one thing that I can't explain. After I ran one step of minimization of a TIP3P water, the output bond energy for this water is 9.9065 kcal/mol. However, the two OH distances are 0.9566 Å and the HH distance is 1.5136 Å, which are very close to the equilibrated distances in the forcefield parameter file (parm10.dat). If I put these values into the bond energy expression stated in the AMBER manual, SUM(kb(r-r0)2), using the force constants and equilibrium distances in the parameter file, I got a value of 0.00042 for the bond energy. Does anyone know why the program give 9,9065 for bond energy in the output file?
Thanks a lot,
Sixue
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Received on Tue Feb 24 2015 - 12:00:28 PST
