[AMBER] Shearing useful tips for adding ions to biomolecular simulations

From: Matias Machado <mmachado.pasteur.edu.uy>
Date: Tue, 18 Feb 2020 15:13:54 -0300 (UYT)

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


 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

Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

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Received on Tue Feb 18 2020 - 10:30:01 PST
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