Well the charmm GUI automatically does this and tells you how many ions will be added to reach the specified salt concentration.
However it is a straightforward calculation to check the result from the number of water molecules in your system:
n = c x NA x V
Where c is concentration (eg. 0.15 M), NA is the Avogadro constant and V is water volume (no. waters x 30 A^3 - approx TIP3P water volume at 303 K, remember to convert to litres).
Cheers,
Callum
________________________________________
From: Fabian gmail <fabian.glaser.gmail.com>
Sent: Tuesday, March 29, 2016 6:33 AM
To: AMBER Mailing List
Subject: [AMBER] salt concentration KCl
Hi,
How can I calculate the number of KCL ions necessary to add to a membrane system to obtain an ion concentration of 0.15M KCl ???
Is there an amber command to do that?
Thanks a lot,
Fabian
Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
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Received on Tue Mar 29 2016 - 06:30:03 PDT
