Your answer clarified a lot. Now I see why you had this command "set default Dielectric xx". It might be useful. The manual needs to be re-written so the readers can know this affects the addIons command, not the parm files.
Thanks al lot! I was waiting for an answer.
> -----Original Message-----
> From: David A Case [mailto:case.biomaps.rutgers.edu]
> Sent: Thursday, September 15, 2011 2:04 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] tleap command "set default Dielectric constant"
> not valid?
>
> On Thu, Sep 15, 2011, Yongmei Wang (ywang) wrote:
> >
> > The AMBERtool manual 1.5, describes a command,
> >
> > set default Dielectric constant (or distance)
> >
> > I am pretty certain this command does not work. For I have tested
> with a
> > tleap script file, with that argument set to constant or distance..
> it
> > produced exactly the same Parm files in both cases, and the same parm
> > file when I delete that line from the script file. So.. could anyone
> > confirm with me that this command is not valid? (I am using AMBER10)
>
> This command (which is so little used we should probably retire it)
> determines
> how addIons places ions into an electrostatic field. As you note, it
> doesn't
> have anything to do with how subsequent programs handle electrostatics,
> and
> hence has no effect on the prmtop file.
>
> The manual does say that this pertains to how electrostatic calcuations
> *in
> LEaP* are handled, but I agree that we could add comments to make this
> clearer.
>
> > Also under the next section when you explain eedmeth=5 option under
> > Ewald summation. I would suggest you change the wording there. The
> > distance-dependent dielectric you are using is the following function
> >
> > epsilon(r)=epsilon_0 * r; (epsilon(r) stands for distance dependent
> > dielectric constant,epsilon_0 is whatever the dielectric constant
> > user specifies). As a result, the electrostatic interaction has
> > 1/r^2 dependence. This function is used for direct part of Columb
> > Interaction. But I am not clear about the long-range part of
> > Coloumb interaction (the part handled by PME). Does PME considers
> > distance-dependent dieletric effect for the long-range electrostatic
> > interaction?
>
> As the manual states, "the last two options [eedmeth=4 and 5] are
> intended for
> non-periodic calculations where no reciprocal term is computed." Your
> suggested wording for the direct sum has some merit.
>
> ...thx...dac
>
>
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Received on Thu Sep 15 2011 - 12:30:04 PDT
