On Wed, Feb 25, 2015, Zhang, Sixue wrote:
> Thanks for the help. I resolved this issue. Some parameters are wrong
> in my topology file. After I corrected them, it gives the energy of
> 0.00021, which is half of the energy I calculated by hand. I guess the
> program adds 1/2 in front of the kb(r-r0)^2 when it gives the final bond
> energy. Am I right?
No, this does not sound correct. The Amber bond energy term does not include
the 1/2 factor. You might want to add print statements to the bond() routine
(in ene.F90) to print out the individual terms.
...dac
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Received on Wed Feb 25 2015 - 06:00:06 PST
