Re: [AMBER] randomly place counterions

From: Kevin Hauser <>
Date: Wed, 2 Mar 2011 11:52:10 -0500


> Maybe I miss something - but wouldn't it be just possible to calculate the
> number of ions from the number of solvating water molecules?

The problem is density, as was noted earlier in the thread. I should've
mentioned that if you're working with an octahedral shell of water, the
volume leap prints, apparently, seems to be a bit off, so you'd have to
calculate the *starting volume by hand, based on the edge-length of the
shell (or equilibrated edge-length as it were).

> Yes - then one
> would have to run leap twice as well, but this is certainly the least
> cost-intensive part of the whole procedure :-)

Indeed. I probably shouldn't do this, but as far as I can tell, experimental
lab's have trouble figuring out exactly how many ions are where, in relation
to the solute with atomic-scale accuracy. So, if you're trying to match some
experiment (with a well-designed simulation setup) that used 1M KCl, your
simulation could contain 111 K+/ 123 Cl- ions as per volume/charge of your
system. You would know when and where each ion is. However, it could be
possible that the equivalent scenario in the experiment would have 222 K+ /
273 Cl- ions in that volume at some instant in time, with very diffuse
concentration far away from the solute, in the bulk.

Take away message: everything depends on your goal - what needs to be
controlled, what needs testing, how you plan to validate experimentally,
etcetera :^)

AMBER mailing list
Received on Wed Mar 02 2011 - 09:00:03 PST
Custom Search