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
> >>
> >>
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> >>
> >
> >
>
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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> 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 - 06:30:04 PDT
