On Tue, May 5, 2015 at 2:54 AM, Chinh Su Tran To <chinh.sutranto.gmail.com>
wrote:
> Dear Amber user,
>
> Im setting my Implicit solvent simulation using ALPB for comformational
> sampling. I wanna change the solvent dielectric constant (say epsilon=20
> instead of the default 80), but I encountered some confusing understanding
> between "extdiel" (default is 78.5) and "epsout" (default is 80).
>
> I search for it and found (here
> http://www.teokem.lu.se/~ulf/Methods/qmmm_pbsa.html) that "extdiel" is
> used
> in GB while "epsout" is used for PB calculation? Is it true and why is it?
>
Yes, this is true. The two codes were written by different (groups of)
people, and they used different variable names.
> Any difference between them as they are both the solvent dielectric
> constant?
>
The difference you pointed out above -- extdiel is the EXTernal DIELectric
constant for GB calculations, while epsout is the EPSilon OUTside the
solvent (i.e., the external dielectric constant) for PB calculations.
Note that epsout is a variable in the &pb namelist, while extdiel belongs
in &cntrl.
I believe ALPB uses the GB code, so extdiel is the appropriate variable to
use.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue May 05 2015 - 05:30:02 PDT
