On Tue, Feb 24, 2015 at 2:37 PM, Zhang, Sixue <szhang74.illinois.edu> wrote:
> There is typo in my previous email, it's 9.9065 instead of 9,9065. Sorry
> about that.
>
> -----Original Message-----
> From: Zhang, Sixue [mailto:szhang74.illinois.edu]
> Sent: 2015年2月24日 13:31
> To: AMBER Mailing List
> Subject: [AMBER] Bond Energy Term for a TIP3P Water
>
> 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?
>
There are 3 bonds in a TIP3P water: O-H1, O-H2, and H1-H2. Make sure you
add in all 3 contributions.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 24 2015 - 12:00:32 PST
