AMBER Archive (2008)

Subject: Re: AMBER: Is there an easy way to calculate the electric field at the center of a group of atoms

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon Dec 01 2008 - 09:34:47 CST

On Thu, Nov 27, 2008, Ye Mei wrote:
>
> Can anyone tell me that if there is an easy way to calculate the electric
> field at the center of a group of atoms
> from the trajectory of molecular dynamics simulation with periodic boundary?

I'm pretty sure there is no easy way. I know various people have thought
about this, and maybe someone will post a suggestion.

You can get the field at an atomic position by dividing the electrostatic
force by the charge on that atom. Even this requires some modification of the
program -- as a start, set ntmin=5, ntf=7, and set the VDW weighting (section
2.8 of the Users' Manual) to zero. This should leave just the electrostatic
forces. Then you would need to modify the code (probably in force.f) to print
out the forces you need.

...good luck...dac

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