Hi all!
I have performed the MD simulation on aqueous lysozyme solution(withou external electric field) with GROMACS. Now, I want to map the spatial distribution of internal electrostatic force field.
I tried to calculate the electrostatic potential at given position(rRef) by summing up the Coulomb potentials generated by all charged atoms(N) in the simulation box, as the following equation. Obviously, only atioms in the original box were taken into account here. However, in MD simulation, the PME method was used for electrostatic force, which means not only atoms in simulation box but also in the mirror boxes were considered. So, I wonder whether this method will cause notabe mistakes?
Is there better way to tackle this problem?Thanks in advance for your advice.
Hi Zhaoxi Sun Thanks very much for you time and answer!
I am using a cubic box of side length ~9nm. I estimated the Coulomb potentials generated by an elementary charge, as shown in the attached picture. It seems that the eletrostatic potential has almostly decreased to 0 at half box length . So, it might be acceptable to neglect the effect of atoms from distant image boxes and only to consider the closest periodic image, as what you suggested.
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