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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--
*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 - 06:30:03 PDT
