Hello,
My comments are below:
On Tue, Jul 27, 2010 at 11:18 PM, Wookyung Yu <sfcywk.gmail.com> wrote:
> Hello!
>
> 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. "
>
The model has been parameterized to reproduce experimental data for
solvation energies, etc. See the original papers cited in the Amber manual
for a more detailed description of the development of the methods.
> If I do MD simulation using another dielectric constant,
> then It's incorrect result?
>
It's not necessarily incorrect, but it will have to be validated in the same
way that the original parameters were validated.
> As I know, in real protein, dielectric constant is not 1 .
>
I've seen values of 2 to 4 to account for electronic polarizability.
However, GB was parameterized with indiel=1 and extdiel=80 (or 78.5, I don't
remember which), so unless you plan to redo the validation using different
values, you should probably use the defaults. Changing intdiel is probably
more appropriate for PB calculations since that's a more formally exact
theory without the parameterization inherent in GB.
> 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."
>
> If I use pmemd.cuda , It's impossible to use another dielectric constant?
>
That's what the error message says, so yes.
Hope this helps,
Jason
>
> Thanks in advance.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 28 2010 - 05:30:03 PDT
