this is well covered in the tutorials- maybe you can tell us which part of
the tutorial is confusing.
http://ambermd.org/tutorials/
for example, even the very first tutorial shows all of the commands needed
to add explicit water.
I still don't understand your questions about dielectric- perhaps you can
work with a colleague that has better English skills? sorry but I'm just
having trouble understanding your question.
On Wed, Mar 10, 2010 at 9:02 AM, Pallavi Mohanty
<pallavipmohanty.gmail.com>wrote:
> 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
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
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> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Regards,
> > >
> > > Pallavi Mohanty
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Regards,
>
> Pallavi Mohanty
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> AMBER mailing list
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>
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Received on Wed Mar 10 2010 - 06:30:04 PST
