charmm

parameters

Value	One or more file names
Default	None

Give the CHARMM force field parameter file names (paths may be included). There can be more than one files:

charmm
  parameters par_all35_ethers.prm /home/zhang/userdef/par_all35_proteins.prm   
end

Note that if the same term, say bond CT-CT, appears in more than one parameter files, then the latter one will overwrite the previous ones.

topology

Value	A file name
Default	None

Give the topology file name of the molecule in PSF format (path may be included).

scaling14

Value	A real number
Default	1.0

Define the scaling factor for electrostatic interactions of 1-4 term.

rcutoff

Value	A real number
Default	15.0

Define the distance in Angstrom to cutoff non-bonded interactions.

If rswitch is larger than rcutoff, switching function will not be used and no cutoff is applied on long range forces.

rswitch

Value	A real number
Default	10.0

Define the distance in Angstrom to activate switching function.

If rswitch is larger than rcutoff, switching function will not be used and no cutoff is applied on long range forces.

use_PBC

Turn on periodic boundary condition for the system. If this option is not present, the system will be a non-periodic, gas phase one.

Lbox

Value	Three real numbers
Default	0. 0. 0.

When use_PBC is present, this option gives the lattice lengths along X, Y, and Z direction in Angstrom.

charmm
  use_PBC
  Lbox 86 86 86
end

This creates a simulation box of 86 Angstrom x 86 Angstrom x 86 Angstrom.

electrostatic

Value	Cutoff Cutoff scheme for gas phase or periodic systems.
	PME Particle mesh Ewald (PME) method. Only available for periodic systems.
Default	Cutoff

Assign the scheme to calculate electrostatic interaction.

For gas phase, Cutoff is the only possible way. For periodic systems, it is recommended to use PME.

PMEk

Value	Three integers
Default	64 64 64

Assign the number of grids for PME long range force calculations. It is recommended that the number should be chosen as an integer close to the lattice length while is a multiply of only 2,3 and/or 5. For example, if Lbox is 109. 109. 77, then PMEk can be set to 108 108 80.