[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
Greetings,
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
\vec{r}.
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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