[gmx-users] Calculating the electrostatic potential at a point over time

Andrew DeYoung adeyoung at andrew.cmu.edu
Wed Mar 28 03:13:29 CEST 2012


Is it possible to determine the electric potential at the location of an
atom, relative to infinity?  From physics, I think that electric potential
(relative to infinity) at the position vector \vec{r} DUE TO a point charge
q located at \vec{r'}, is given by, in SI units:

V_q(\vec{r}) = q/(4*pi*epsilon0*|\vec{r}-\vec{r'}|)

where |\vec{r}-\vec{r'}| is the magnitude of the vector between the position
of the source charge (\vec{r'}) and the observation location (\vec{r}).  

I would like to sum over that formula to determine the electric potential AT
the position of an atom located at \vec{r} DUE TO all the other partial
charges in the system:

V(\vec{r}) = \sum_i ((q_i)/(4*pi*epsilon0*|\vec{r}-\vec{r'_i}|))

where the sum is over all charges in the system except the charge at

If a point charge Q is at \vec{r}, then I think that this is just the
electrostatic energy of Q, divided by Q.  

Is there any way to calculate this in Gromacs?  I know that g_potential
computes the electrostatic potential across the box (by integrating the
Poisson equation, it seems), but I want to compute just the electrostatic
potential at the location of a single atom.  

Thank you so VERY much for your time! 

Andrew DeYoung
Carnegie Mellon University

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