Re: PME non-zero charge

From: Roman Petrenko (
Date: Thu Nov 06 2008 - 19:42:25 CST

Thanks for quick answers,
any other expert opinions? reference articles? unfortunately, it
affects 50% of my trajectories, so i really want to know what's going
on with infinite charge summation :(

On Thu, Nov 6, 2008 at 7:09 PM, Peter Freddolino <> wrote:
> My understanding is that NAMD's approach to PME with a non-neutral unit cell
> effectively assumes the presence of a uniform, neutralizing charge density
> throughout the periodic cell (which gets rid of the otherwise divergent
> terms). Because the charge density is uniform the forces (and thus dynamics)
> of the system are correct/unaffected, but the calculated energies will be
> offset from the correct values, and even with this correction the
> non-neutral system will be more susceptible to several PME-related artifacts
> (see, for example, JPCB 108:774 (2004)).
> Peter
> Roman Petrenko wrote:
>> Dear namd developers,
>> how does namd handles PME calculations of systems with non-zero total
>> charge?
>> and second related question: is there a routine for automatically
>> adding counter-ions to proper places?

Roman Petrenko.
Physics Department
University of Cincinnati

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