From: Todd Trimble (TODD.TRIMBLE_at_asu.edu)
Date: Mon Nov 13 2006 - 10:44:29 CST
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 and a Langevin
barostat and thermostat. When I run a long simulation (4ns, 2fs step),
near the end of the simulation the system volume increases rapidly and
my water box blows up. The energy in the MISC column decreases pretty
linearly until the end when it suddenly takes off. If I run shorter
simulations the volume will increase slowly and the MISC energy will
decrease linearly as in the long run. However, when I start a new
simulation from the restart values of the previous run, the MISC energy
immediately jumps up and the volume quickly decays to values close to
the starting values of the previous run. So it seems like I can keep
the box from blowing apart by breaking up a simulation into multiple
runs, but I don't understand this behavior and so I don't trust the
results.
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 PME grid size is around 1 ang. or less. I am also
using 2 fs/step with all H bonds set to rigid.
Has anyone else had similar problems? Any advice would be greatly
appreciated.
Todd
**********************************************************************
Dr. Todd M. Trimble
Asst. Professor of Research
Center for Applied Nanobioscience at the Biodesign Institute
Arizona State University
todd.trimble_at_asu.edu
work: 480-727-0435
fax: 480-727-8283
**********************************************************************
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