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

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

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,

------------------------------------
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
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