VMD PMEPot Plugin, Version 1.0

The 'pmepot' plugin evaluates the reciprocal sum of the smooth particle-mesh Ewald method (PME), producing a smoothed electrostatic potential grid, and writes it to a DX file, and reads it into the molecule. The smoothing is a natural result of the PME algorithm in which point charges are spread into Gaussians with sharpness controlled by the Ewald factor. Only the reciprocal sum is calculated, there is no direct (short-range) term. Charge information must be available for the molecule (PDB2PQR can generate a charge-containing PQR file from a PDB file or ID). The PME algorithm requires a periodic cell, although a non-periodic potential may be approximated by making the cell significantly larger than the dimensions of the molecule (padding the bounding box). Periodic cell information is taken from VMD, the bounding box, a NAMD .xsc file, or as specified by the user.

This method is described in detail here. Please include this reference in published work using the PME plugin: "Imaging alpha-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability and the electrostatic potential map". Aleksij Aksimentiev and Klaus Schulten. Biophysical Journal, 88:3745-3761, 2005.

Decalanine Example

package require pmepot

set mol [mol new alanin.psf type psf waitfor all]
mol addfile alanin.pdb type pdb waitfor all

pmepot -mol $mol -ewaldfactor 5.0 -grid 0.5

Periodic Simulation Example

package require pmepot

set mol [mol new msp1_cell.psf type psf waitfor all]
mol addfile mincell-out.coor type pdb waitfor all

pmepot -mol $mol -xscfile mincell-out.xsc -ewaldfactor 0.25

Command Arguments

usage: pmepot ?-arg val?...
  -mol molid (defaults to top, do not combine with -sel)
  -sel selection (proc returned by atomselect command)
  -frames begin:end or begin:step:end or all or now
  -updatesel yes or no (default) (update selection for each frame)
  -pad d (cell is bounding box plus d on each side)
  -cell {{ox oy oz} {ax ay az} {bx by bz} {cx cy cz}} (o is center)
  -xscfile filename (get cell from NAMD .xsc file)
  -grid {na nb nc} (integer grid dimensions for PME)
  -grid n (integer grid dimension for PME, n > 8)
  -grid resolution (grid resolution for PME in Angstroms)
  -dxfile filename (write potential map to file)
  -loadmol molid or none or same or new (molecule to load data to)
  -ewaldfactor factor (specify ewald factor)