electric field

From: Todd Trimble (TODD.TRIMBLE_at_asu.edu)
Date: Tue Nov 21 2006 - 15:08:11 CST


I have questions about the energy from an applied electric field as
reported in the MISC column. I have been seeing that when I restart a
simulation (ssDNA + counterions +water), the MISC energy jumps back up
to a value close to the initial value from the previous run. It's not
even close to the final value of the previous run. I ran a test
simulation with a single chlorine ion in vacuum with an applied field,
and I didn't have the same problem when I restarted a simulation. Also,
the change in the MISC energy corresponded to the energy associated with
the movement of the charge in the E field.

Can anyone tell me why I am seeing this problem with my large system and
not with a single ion? Could this be an artifact related to a massive
reorganization of the patches and the atoms in each patch at the start
of the next run? However, even when I run a simulation on my system
specifying 0 time steps and then take those binary restart files as the
input files for a new simulation, the initial MISC is slightly different
(-4187 versus -4028)!

Also, I understand how the changes in MISC work, but how is the initial
value of MISC determined?
Anyway, I'm thoroughly confused and hope one of you can explain this to
me. Thanks,


Dr. Todd M. Trimble
Center for Applied Nanobioscience at the Biodesign Institute
Arizona State University

work: 480-727-0435
fax: 480-727-8283

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