RE: pressure calculation in applied field

From: Todd Trimble (
Date: Tue Nov 28 2006 - 17:30:21 CST

Hi Brian,

I also should have mentioned that in the restarted NVT simulations the
initial electrostatic energy is right on with the final value from the
previous run (while the MISC energy and the pressure make large jumps).


-----Original Message-----
From: Brian Bennion []
Sent: Tuesday, November 28, 2006 3:06 PM
To: Todd Trimble
Subject: Re: namd-l: pressure calculation in applied field

Hello Todd,

This sounds like a difficult problem (which is why no one has
responded) and appears at first blush to be similar to problems I see
in my membrane simulations
where the box continually expands in one dimension until it crashes
due to pme grid/small patch errors.
I am using namd2.6 which version are you using? You probably stated
this in email #1 but for my sake will you give the machine and
version specifics again?



At 10:36 AM 11/28/2006, you wrote:
>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
>I break up into multiple runs it looks OK. The volume of the box in
>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
>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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