Is anyone aware of a third-party tool to calculate electrostatic potential distributions as 3D maps or along a given vector? Basically, I have a membrane with a hole and would like to plot electrostatic potential along the vector crossing the hole, perpendicularly to the membrane. The box is a hexagonal prism, periodic in all directions. gmx potential is entirely inadequate for this, so I wonder how others have accomplished similar tasks.
you can check out the pmepot plugin for VMD. It can compute the 3D potential and write it to disk, after which you can analyze it.
I’m not sure if this is the same plugin, but there is the PME Electrostatics tool in VMD and it does produce a .dx file (with hexagonal symmetry unfortunately mangled into some orthorhombic thing). Now the question is what to do with that file, given that all I really need is a subzone along a straight line. Is there an existing software that could do this? Chimera seems to be mostly a visualization tool…