sorry for being specific need to ask you made my system in presence of TIP3P
water , qusetion in presence of water i.e EXPLICIT SOLVENT environment which
dielectric need to be considered.Please specify the commands as well
On Wed, Mar 10, 2010 at 5:06 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> it's not clear what you mean by dielectric of 1. you mean only the
> dielectric given by the water model?
> the tutorials show how to run simulations with TIP3P, and the dielectric is
> discussed in the manual (see the dielc variable).
>
>
> On Wed, Mar 10, 2010 at 5:11 AM, Pallavi Mohanty
> <pallavipmohanty.gmail.com>wrote:
>
> > yes i have gone through the tutorial but didnt find appropraite answer
> for
> > my query..again i want to ask the asme question that what parameters i
> need
> > to include if ruuning the equilibration with dilectric = 1 in presence of
> > TIP3P water
> >
> > On Tue, Mar 9, 2010 at 5:01 PM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > there are many tutorials available on the web site at www.ambermd.org.
> > > they
> > > are very helpful.
> > >
> > >
> > > On Mon, Mar 8, 2010 at 11:42 PM, Pallavi Mohanty
> > > <pallavipmohanty.gmail.com>wrote:
> > >
> > > > Need to run Explicit Solvent Models with PME and dielectric 1 for my
> > > > system.Can I know the parameters at at equlibration and production
> > phase
> > > as
> > > > i am pretty new for AMBER
> > > >
> > > > --
> > > > Regards,
> > > >
> > > > Pallavi Mohanty
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> > >
> >
> >
> >
> > --
> > Regards,
> >
> > Pallavi Mohanty
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Regards,
Pallavi Mohanty
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Received on Wed Mar 10 2010 - 06:30:03 PST
