Dear Amberites,
We want to share some simple tips for setting correct macroscopic salt concentrations in MD simulations.
We recently published a paper introducing an intuitive shortcut to SLTCAP to derive the correct amount of ions according to the salt concentration and the solute's charge [
https://doi.org/10.1021/acs.jctc.9b00953].
The method was tested against osmostat simulations, and it proves to be valid for >98% of the available PDB structures at [NaCl]=0.15M.
The SPLIT method is as follows:
--------------------------------
1) Calculate the expected number of ions (No) for a macroscopic salt concentration (Co, in molar units) in a simulation box of Nw water molecules:
No = Nw*Co/56 # Best proved No estimator
2) Get the actual number of positive (N+) and negative (N-) monovalent ions to add in the box due to the the solute's charge (Q):
N+ = No - Q/2 # round up in case of odd Q (e.g. N+ = 2.5 ~ 3)
N- = No + Q/2 # round up in case of odd Q (e.g. N- = 5.5 ~ 6)
Yes! That's it, no more difficult equations to remember, just SPLIT the solute's charge in two... no more excuses to do it right!
Beware, the method is only valid whenever No/Q >= 1.
Practical example:
---------------------------------
Lysozyme (PDB: 2VB1), Q = +8e, Water box 12Å => Nw ~ 7000 molecules, [NaCl]=0.15M:
No = 7000*0.15/56 ~19 => No/Q > 1
Then,
Na+ = 19 -(+8)/2 = 15
Cl- = 19 +(+8)/2 = 23
---------------------------------
Our intention is to help and promote the correct setup of MD simulation.
Hope you find it useful.
All the best,
Matias Machado
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
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Received on Tue Feb 18 2020 - 10:30:01 PST
