From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Dec 09 2006 - 14:19:01 CST
Hi Todd,
I'll ask around here and see if anyone who works with E fields has seen
something similar. In the meantime, I would recommend that you try to
reproduce this with NAMD2.6.
Peter
Todd Trimble wrote:
> Hi All,
>
> I've been having problems related to the pressure calculation in namd
> v2.5 when an electric field is applied. I decided to run some tests
> using a cubic waterbox w/ pbc and a couple ions (system is overall
> neutral). After equilibration at constant volume and temp, I ran 2
> production runs at constant NVT: 1 with the field switched off and 1
> with the field on. Plots of the pressure are shown in the attached
> figures (3ns total simulation times). The first plot (E field off)
> shows a constant average pressure while the second plot (E field on)
> shows a systematic increase in average pressure. I don't know the
> details of the pressure calculation and it's not spelled out in the
> manual. I would assume that the contributions to the virial from the
> forces due to the field are treated in the same way as those from the
> interparticle forces. I don't see how this behavior can be real. Also,
> if I do the same test in a waterbox without the ions, the pressure shows
> a constant average regardless of whether a field is on or off.
>
> The last plot shows what happens when I use binary restart files
> (coordinates, velocities and .xsc) to continue the simulation with the
> E-field turned on. The average pressure drops back down to a value
> close to that from the beginning of the preceding simulation. After
> that, the average pressure drifts upward again. This just doesn't make
> any sense.
>
> If anybody has any ideas or comments, please let me know.
>
> Peter, can you forward this to the namd developers? Thanks,
>
> 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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