Sorry. 30 angstrom drop of water.
Jim Kress
-----Original Message-----
From: James Kress [mailto:jimkress_58.kressworks.org]
Sent: Friday, April 21, 2017 12:53 PM
To: 'AMBER Mailing List' <amber.ambermd.org>
Subject: RE: [AMBER] Internal dielectric constant and pmemd
Perhaps you should explain the experiment you performed and its results to
see if the simulation you are trying to perform corresponds to the
experiment.
I have a hard time believing that a 3 angstrom diameter drop of H2O has a
dielectric constant that differs significantly from 1.
Jim Kress
-----Original Message-----
From: Samaneh Ghassabi Kondalaji [mailto:saghassabikondalaji.mix.wvu.edu]
Sent: Friday, April 21, 2017 9:36 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Internal dielectric constant and pmemd
Unfortunately the process I am simulating says otherwise from experimental
point of view. I determined the values and now I need to apply them to my
system.
On Fri, Apr 21, 2017 at 9:26 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Sam:
>
> you said that:
>
> "I need to change the dielectric constant of water in this droplet
> from 78.5 to 1 and at the same time preserve the vacuum."
>
> And what I am telling you is that the dielectric constant of your
> system is already equal to 1 for the water, so I do not understand
> what your issue is.
> There is nothing to change from 78.5 to 1, it is already 1.
>
> adrian
>
>
> On 4/21/17 9:21 AM, Samaneh Ghassabi Kondalaji wrote:
> > I understand what igb=6 does to my system in terms of
> > dielectric constant and I actually need the value of one as I am in
> > vacuum, but Is there ANY way in pmemd that I can have two different
> > dielectric
> constants (
> > it seems unrealistic but it is what it has to be!).
> > Cheers,
> > Sam
> >
> > On Fri, Apr 21, 2017 at 9:14 AM, Adrian Roitberg <roitberg.ufl.edu>
> wrote:
> >
> >> The dielectric constant of your system will be ONE without you
> >> doing anything.
> >>
> >> The fact that you are using igb=6 immediately does that, and the
> >> fact that you have water molecules does not make any difference.
> >>
> >> adrian
> >>
> >>
> >> On 4/21/17 9:11 AM, Samaneh Ghassabi Kondalaji wrote:
> >>> Yes, it seems very confusing but my system is a peptide in a
> large
> >>> water droplet (~3.0 nm in diameter) present in vacuum and I need
> >>> the
> >> water
> >>> molecules to leave the system gradually. I use igb=6 so I can use
> >>> pmemd
> >> for
> >>> vacuum simulations. I need to change the dielectric constant of
> >>> water
> in
> >>> this droplet from 78.5 to 1 and at the same time preserve the vacuum.
> >> Can I
> >>> just do it with dielec or I will need external, internal
> >>> dielectric parameters?
> >>> Best
> >>> Sam
> >>>
> >>> On Fri, Apr 21, 2017 at 8:04 AM, David Case
> >>> <david.case.rutgers.edu>
> >> wrote:
> >>>> On Thu, Apr 20, 2017, Samaneh Ghassabi Kondalaji wrote:
> >>>>
> >>>>> I am performing a simulation that requires the change of
> internal
> >>>>> dielectric constant and of course the non-default values of
> >>>>> intdiel
> are
> >>>> not
> >>>>> supported in pmemd. I was wondering if anyone has found a way
> >>>>> around
> >> it?
> >>>>> Has there been a bugfix recently that fixes this? Is it possible
> >>>>> to
> use
> >>>> the
> >>>>> dielct value of matching the desired intdiel but use a different
> >> extdiel
> >>>> or
> >>>>> the dielct parameter will override the extdiel? I am using pmemd
> >>>>> and
> >>>> igb=6
> >>>>> to simulate a very large system in the gas phase and I am not
> >>>>> going
> to
> >> be
> >>>>> able to use sander for my purpose.
> >>>> I am confused here: if you are using igb=6, the concepts of a
> "internal"
> >>>> and
> >>>> "external" dielectric don't come into play. Any values you tried
> >>>> to
> >> enter
> >>>> there would be ignored.
> >>>>
> >>>> ....dac
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >> --
> >> Dr. Adrian E. Roitberg
> >> University of Florida Research Foundation Professor Department of
> >> Chemistry University of Florida roitberg.ufl.edu
> >> 352-392-6972
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor Department of
> Chemistry University of Florida roitberg.ufl.edu
> 352-392-6972
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Samaneh ghassabi kondalaji*
*PhD student in Chemistry*
*555 CRL, Chemistry department*
*West Virginia University *
*Morgantown, USA*
*E-mail: **saghassabikondalaji.mix.wvu.edu*
<saghassabikondalaji.mix.wvu.edu>
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Received on Fri Apr 21 2017 - 10:00:03 PDT
