From: Brian Bennion (bennion1_at_llnl.gov)
Date: Tue Nov 28 2006 - 16:06:10 CST
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?
Thanks
Brian
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
>charm.
>
>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
>
>todd.trimble_at_asu.edu
>work: 480-727-0435
>fax: 480-727-8283
>**********************************************************************
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:13 CST