AMBER Archive (2007)

Subject: Re: AMBER: electric field calculation

From: lishan yao (yaolisha_at_msu.edu)
Date: Thu May 31 2007 - 08:33:20 CDT

Thank you David. Since I want to compare the field on different nitrogens
and 1-2 and 1-3 electrostatics should be very similar on each site, I can
simply treat 1-2 and 1-3 as my background (hopefully o.k.). One question is
how to extract this electrostatics force from simulation?
Is it explained on the manual?

Best,
Lishan

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Wednesday, May 30, 2007 19:14
Subject: Re: AMBER: electric field calculation

> On Wed, May 30, 2007, lishan yao wrote:
>
> > I am running MD simulation for a small protein with explicit
water. I
> > want to find out the electric field on each backbone Nitrogen atom. Is
there
> > a way to do it?(My speculation is that it may not work with PME method
> > switch on in my simulation).
> >
>
> This is not printed out in the current code, so you will have to extract
> the total electrostatic force on each nitrogen, then divide by the
nitrogen
> partial charge. Be aware that molecular mechanics force fields skip 1-2
and
> 1-3 electrostatic interactions, so you may need to think about how to
> compensate for this.
>
> Since we are doing some similar things, this facility may be incorporated
into
> the next release of Amber (I know: not much help for now!)
>
> ....dac
>
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