pressure calculation in applied field

From: Todd Trimble (
Date: Tue Nov 28 2006 - 12:36:51 CST

Hi All,

Well I haven't got any response so far, but maybe the 10th time is the

I'm running an NPT simulation of an ssDNA molecule tethered at one end
and surrounded by water and counterions. I apply an electric field as
well. If my run has a large number of steps the box will explode but if
I break up into multiple runs it looks OK. The volume of the box in any
run increases pretty linearly up until failure. I figured the pressure
control might be the problem, so I ran NVT simulations. I expected the
pressure to be pretty constant, although the change in DNA conformation
should affect the pressure through the interparticle force part of the
virial. Well, the pressure showed a systematic increase and doesn't
level off. Even worse, when I use the binary restart files in a new
simulation, the pressure drops way down again. How can this be when the
virial depends only on the coordinates and the velocities and these are
identical to those at the end of the previous simulation? These
problems with pressure calculation must be responsible for my exploding
NPT system. The calculated pressure keeps increasing, which forces the
volume to increase in order to maintain constant pressure until the
system is unstable.

Is the pressure calculation not reliable in the presence of an applied
field or forces?

Thanks, Todd

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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