On Thu, Jun 23, 2011, Marek Maly wrote:
> > I want to do normal analyses of vacuum conformations of the given
> > molecule.
Then set igb=0 and don't change DIELC from its default value.
(The only real use I know of for setting is DIELC to something other than 1 is
for calculations that use a distance dependent dielectric, where epsilon = 4r.
This was popular a long time ago (before the development of GB and other
implicit solvent models), but never had much to recommend it.)
Amber, and other simulation packages, indeed offer lots of options, but
that often just gives users enough rope to hang themselves. As an example:
you can say "I want to d normal [mode] analysis in vacuum...", and
apparently do that. But you should remember that the potentials were
parameterized for condensed phase simulations, and often do a very poor
job of representing what would really happen in vacuum. So the code's
ability to (apparently) carry out a vacuum simulation should be treated
with appropriate caution.
In general, changing parameters a long way from their default values, (such as
changing EXTDIEL in gb to 1 from its default value of 78) is dangerous.
Experimentation is instructive (and encouraged!), but please remember that the
range of validity of simple force field models is limited.
...dac
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Received on Thu Jun 23 2011 - 09:30:04 PDT
