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How to calculate the concentration of peptide or protein in a simulation box?
In general, concentration of molecule A in water can be calculated in the following way, n mol_A/n mol_water = [conc]_A/ 55.6 where 55.6 is mol water in a liter an n_mol number of molecule in the simulation box. This is meaningful only when several A molecules are in water solution.
If after concentration within the volume you simulated then simply use the equation for molar concentration:
C = n/V
n = number of moles within simulation
V = simulation box volume in litres
n = number of molecules / Na
Na = Avagadro's Constant