electric field

From: Todd Trimble (TODD.TRIMBLE_at_asu.edu)
Date: Thu Nov 16 2006 - 11:57:25 CST

Hi All,

I'm running a simulation on DNA in an electric field in NPT ensemble. I
haven't included any time dependence in the field, the pressure and
temperature are fixed at 1atm and 300K with Langevin barostat and
thermostat, electrostatics are treated with PME algorithm, and I'm using
PBC. 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. I've seen
several other posts about this problem in the archives, but no real
answers. Could you please let me know if you have any ideas why this is
happening? And how is the energy in the MISC column calculated (maybe
one of you developers could answer this)? 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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