AMBER Archive (2004)

Subject: Re: AMBER: Regarding Dielectric Constant in AMBER8

From: pande.vineet_at_fc.up.pt
Date: Thu Nov 25 2004 - 10:03:27 CST

Thanks..
that message says:

use 'dielc=xx' in the &cntrl namelist together with 'eedmeth=5' in the
&ewald namlist.

But, I donīt want to evoke PME and PBCs, I would like to use Distance dependent
dielec. for non-periodic calculations, just like we could do in previous
versions by using IDIEL...
Regards,
Vineet
Quoting Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu>:

> the first and second results from a google search for
> "amber distance dependent dielectric"
> point to the answer in the amber archive:
>
> http://amber.ch.ic.ac.uk/archive/200404/0244.html
>
> pande.vineet_at_fc.up.pt wrote:
>
> >Dear AMBER Users:
> >
> >This question is about specifying the type of DIELECTRIC in Sander
> calculations.
> >
> >When I use PBCs and PME, and specify dielc = 1.0, it refers to a constant
> >dielctric, which is reasonable in this case..
> >
> >BUT, if I want to perform a minimization with a DISTANCE DEPENDENT
> DIELCTRIC, in
> >AMBER8 what shall I do? Because IDIEL flag no longer works in AMBER8. Is it
> that
> >if I specify dielc = 1.0, and do not use PBCs/PME, it would refer by default
> to
> >a "distance-dependent" and not a "constant"? And then how to switch on to
> >"constant" ,imagining that we are doing a stochastic simulation and we donīt
> >apply PBCs..
> >
> >Thanks in advance!
> >Vineet Pande
> >
> >
> >
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