On Fri, Aug 13, 2010, sunita gupta wrote:
>
> I am going through a tutorial of relative binding energy calculation between
> benzene and phenol (
> http://ambermd.org/tutorials/advanced/tutorial9/setup.html)
> I am using the exact protocol for generating topology and coordinate file
> for benzene molecule....the %FLAG radii is having different radii value for
> water molecules.
> My values are coming out to be 1.50000000E+00 8.00000000E-01
> 8.00000000E-01 for O-H1-H2 ....where as the topology file present in the
> tutorial are having different values..ie...1.50000000E+00 8.00000000E-01
> 1.20000000E+00 for O-H1-H2...
There was a bug in the code when the tutorial was put togther, which I think
is now fixed.
>
> I did not understand why the two hydrogen's of water molecule should have
> different radii..?
They should not.
> Kindly suggest...as because of this difference my results are varying a lot
> while vdw decoupling step.
The values of the radii are only relevant for implicit solvent calculations,
which should never have waters anyway (which is why the bug was not
immediately noticed.) Nothing that you should be doing in tutorial 10
uses these radii, so if you are having troubles, it probably comes from some
different source. Note that to get converged values, you need more sampling
and more lambda points than used in the tutorial -- those files are just to
get you started....
....dac
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Received on Fri Aug 13 2010 - 07:00:05 PDT
