Hi Kshatresh,
I am sorry but I have not worked with electric fields except their
application on a bilayer membrane.
Good luck with finding answers.
Chetna
On Wed, Jul 24, 2019 at 1:56 PM Kshatresh Dutta Dubey <kshatresh.gmail.com>
wrote:
> Dear Chetana,
>
> Thanks for your reply. However, I wish to see some references which tell
> about the formulation/modelling of the external electric field in MD
> simulations. For example, to apply an external electric field we must have
> a source ( such as two charged plates or electrodes), therefore what is the
> source of this external field. How does current implementation study the
> screening effect by the solvent? The effect of the electric field will
> decrease if we move away from the plates/electrodes so how does Amber
> account such distance-dependent nature of electric field? I will appreciate
> if you or anyone can refer any literature related to these queries.
>
> Best regards
> Kshatresh
>
> On Wed, Jul 24, 2019 at 5:07 PM Chetna Tyagi <cheta231.gmail.com> wrote:
>
> > Dear Kshatresh,
> >
> > In Amber, you can apply an external electric field using the efx, efy, or
> > efz parameter (mdin file) that defines the intensity of field in Kcal
> mol−1
> > Å−1 *e*−1
> > In the paper,
> > https://www.sciencedirect.com/science/article/pii/S0006349516302818
> they
> > applied an external field with intensity *E* of 0.180 Kcal mol−1 Å−1
> *e*−1
> > in the *z* axis.
> >
> > The x,y and z directions state the direction of applied field.
> >
> > Hope this helps.
> >
> > Chetna
> >
> > On Wed, Jul 24, 2019 at 6:15 AM Kshatresh Dutta Dubey <
> kshatresh.gmail.com
> > >
> > wrote:
> >
> > > Dear Users,
> > >
> > > I want to see how does Amber apply an external electric field during MD
> > > simulations. I will appreciate if someone could provide me some
> > references
> > > where I can see the formulation and implementations of the external
> > > electric field.
> > >
> > > Best regards
> > > Kshatresh
> > > --
> > > With best regards
> > >
> > >
> >
> ************************************************************************************************
> > > Dr. Kshatresh Dutta Dubey
> > > Department of Chemistry
> > > School of Natural Sciences
> > > Shiv Nadar University
> > > Gautam Budhha Nagar
> > > Uttar Pradesh-201314
> > > India
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > Best wishes
> > Chetna
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> With best regards
>
> ************************************************************************************************
> Dr. Kshatresh Dutta Dubey
> Department of Chemistry
> School of Natural Sciences
> Shiv Nadar University
> Gautam Budhha Nagar
> Uttar Pradesh-201314
> India
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best wishes
Chetna
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Received on Wed Jul 24 2019 - 05:30:01 PDT
