On Wed, Jul 28, 2010, Wookyung Yu wrote:
>
> I want to do MD simulation on differenect dielectric constant. with GB and
> pmemd.cuda.
>
> But Manual said
> intdiel
> Sets the interior dielectric constant of the molecule of interest.
> Default is 1.0. Othervalues have not been extensively tested.
>
> What's the meaning of " Othervalues have not been extensively tested. "
It means more or less exactly what it says: use of non-default values of
intdiel is a research topic, and you should expect to have to study the
options and results carefully.
> As I know, in real protein, dielectric constant is not 1 .
But many of the motions that contribute to the "real" dielectric constant
are being explcitly modeled in the GB/MD simulation. Furthermore, the
charge model was designed for dielectric 1, and things like H-bond
energies can be wrong if you use charges designed for epsilon=1 in some
other model.
Of course, people are encouraged to run test caclulations and learn new things
about force fields and solvation models. Just be aware that you would be
breaking some new ground here.
>
> And another question is
> If I set "intdiel" parameter in pmemd.cuda.
> the error message is occurred.
>
> "ERROR : Non-default values of intdiel are not supported."
Means what it says; I'm not sure how else to word it to make it more clear.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 28 2010 - 06:00:11 PDT
