AMBER Archive (2005)

Subject: AMBER: External Electric Field

From: Brandon Tefft (bjtefft_at_yahoo.com)
Date: Tue Feb 01 2005 - 15:30:22 CST

Dear Amber Users,
     I have been trying to run a simulation in which a
DNA molecule is drawn through a silicon dioxide
nanopore by an external electric field. Up until this
point, I have been running the simulation without the
electric field and I would now like to add it. I'm
not sure if this is possible. Perhaps an alternative
is to attach a permanent force to the
negatively-charged phosphate groups on the DNA.
     There have been some e-mails on this topic in the
past and a reference to a paper (Tieleman 2001
Biophysical Journal), but I am not finding these to be
very helpful. Can someone please explain how I can
add an external electric field or attach a force to a
group of atoms in Amber? Please note that my
simulation is periodic so I cannot simply add charged
ions to attract the DNA through the pore.

Thank you,
Brandon Tefft

Senior in General Engineering
Beckman Institute
University of Illinois at Urbana-Champaign

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