splitting up long run leads to very different DNA conformation in E field

From: Todd Trimble (TODD.TRIMBLE_at_asu.edu)
Date: Thu Jul 13 2006 - 18:40:10 CDT

Hi All,


I am trying to look at the effect of an applied electric field on ssDNA
conformation (one end fixed). The solvent is treated explicitly, along
with counterions that neutralize DNA charge (128 Na + 99 Cl ions). The
ionic strength is high, as is the E field strength (10mV/ang). I'm
using the PME algorithm to handle the electrostatics. The problem I'm
seeing is that I get very different results (i.e. end-to-end distance)
when the simulation is carried out in a single run compared to when I
split it into several shorter runs. The end-to-end distances in the 2
cases are different by about 50%. The shorter simulations use the
restart files (.coor, .vel, .xsc) of the previous simulation. The
temperature and pressure setpoints are 300K and 1atm. The system has
been through an extensive equilibration procedure prior to turning on
the field. The volume of the cell does not seem to change much during
simulation, and the PME grid size is around 1 ang. or less. I am also
using 2 fs/step with all H bonds set to rigid.


The initial electrostatic energy is identical to the final electrostatic
energy from the previous simulation, but the initial potential energy is
a little different than the final value of the previous simulation. I
assumed that this was due to the regeneration of the PME grid at the
start. Because the volume changes so little it's hard to believe that
the generation of a new grid periodically could alter my results so
drastically, but I can't think of anything else that is changing when I
restart a simulation.


Has anyone else had similar problems? Any advice would be greatly


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

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

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