Re: AMBER: Ewald calculation using PME for charged system

From: Wayne Dawson <>
Date: Wed, 10 Mar 2004 12:28:36 +0900

Byungchan Kim wrote
> I am just questioning general stuff. I read the FAQ on the web. But
> still qurious, even though people did not mention how they
> neutralize a system in an article, does it mean that they neutralize
> the system anyway?

I don't know what articles you are referring to specifically. However,
I doubt that the authors (if they know any physics and chemistry at
all), would purposely build a __whole PERIODIC system__ that had a net
excess of charge. Yes the protein may have had a net
positive/negative charge, or the system could contain "extra ions",
but these were surely balanced by an equal number of oppositely
charged ions to make the __SYSTEM__ neutral, although the authors may
not have said so explicitly.

With PBC/PME, you're building something remotely akin to an amorphous
crystal. Crystals have more far variety than a PBC system, but they
are ultimately neutral.

The only place I could see fiddling with a net excess of charge is if
you were studying surface effects in an ultra high vacuum chamber. But
these effects are intrinsicly non-periodic and it would not be
permissible to apply the PME to solve them. An amber-doable
application might be something like assessing the likelihood of
formation of simple amino acids in comets, interplanetary dust, or
something of that nature. But then you would still need to consider
chemical reactions in the simulations.

.... wkd
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Mar 10 2004 - 03:53:00 PST
Custom Search