[gmx-users] calculating ionic strength

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jun 6 14:28:37 CEST 2008


Now imagine your simulation system as a say 1000 nm3 portion of a
liter. For that liter you work out the number of ions and you properly
translate that into an amount of ions you expect in the 1000 nm3. But
then your protein (floating along in the same liter in some small
concentration) crosses your small volume and you have a snapshot of a
simulation system. Will the concentration of ions be what you would
get if you would work out the volume (which is what genion -conc
does)? Or should you consider how many moles of water you have in the
system and work out the stochiometry? And what about the effect of the
protein on the local salt concentration? A lot of homework for that
poor first-year chemistry student.


On Fri, Jun 6, 2008 at 1:53 PM, Miguel Machuqueiro <machuque at itqb.unl.pt> wrote:
> At 12:24 AM 6/6/2008, you wrote:
>> jayant james wrote:
>>> Hi all !!
>>> I want to add 150mM KCl into a cubic box that contains a protein in an
>>> aqueous environment. How am I to calculate as to how? many Ions of K and Cl,
>>> I need to add to bring to the above said salt conc?
>> This sounds like a homework exercise for a first-year chemistry student!
>> Work out the volume, then use the concentration to get a number of ions.
>> Mark
> Hi Mark
> Just out of curiosity... how do you "work out the volume"?
> Miguel
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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