Module MMTK.ForceFields

Submodules:


Class CalphaForceField: Effective harmonic force field for a C-alpha protein model

Constructor: CalphaForceField(cutoff=None, scale_factor=1.)

cutoff

the cutoff for pair interactions, should be at least 2.5 nm

scale_factor

a global scaling factor.

Pair interactions in periodic systems are calculated using the minimum-image convention; the cutoff should therefore never be larger than half the smallest edge length of the elementary cell.

See [Hinsen2000] for a description of this force field.


Class DeformationForceField: Deformation force field for protein normal mode calculations

Constructor: DeformationForceField(range=0.7, cutoff=1.2, factor=46402.)

range

the range parameter

cutoff

the cutoff for pair interactions, should be significantly larger than range.

factor

a global scaling factor.

Pair interactions in periodic systems are calculated using the minimum-image convention; the cutoff should therefore never be larger than half the smallest edge length of the elementary cell.

The pair interaction energy has the form U(r)=|factor|*exp(-(r-0.01)**2/|range|**2). The default value for range is appropriate for a C-alpha model of a protein. See [Hinsen1998] for details.


Class LennardJonesForceField: Lennard-Jones force field for noble gases

Constructor: LennardJonesForceField(cutoff)

cutoff

a cutoff value or None, meaning no cutoff

Pair interactions in periodic systems are calculated using the minimum-image convention; the cutoff should therefore never be larger than half the smallest edge length of the elementary cell.

The Lennard-Jones parameters are taken from the atom attributes LJ_radius and LJ_energy. The pair interaction energy has the form U(r)=4*LJ_energy*((LJ_radius/r)**12-(LJ_radius/r)**6).


Class Amber94ForceField: Amber 94 force field

Constructor: Amber94ForceField(lennard_jones_options, electrostatic_options)

lennard_jones_options

parameters for Lennard-Jones interactions; one of:

electrostatic_options
  • parameters for electrostatic interactions; one of:

  • Pair interactions in periodic systems are calculated using the minimum-image convention; the cutoff should therefore never be larger than half the smallest edge length of the elementary cell.

    For Lennard-Jones interactions, all terms for pairs whose distance exceeds the cutoff are set to zero, without any form of correction. For electrostatic interactions, a charge-neutralizing surface charge density is added around the cutoff sphere in order to reduce cutoff effects [Wolf1999].

    For Ewald summation, there are some additional parameters that can be specified by dictionary entries:

    MMTK provides default values for these parameter which are calculated as a function of the system size. However, these parameters are exaggerated in most cases of practical interest and can lead to excessive calculation times for large systems. It is preferable to determine suitable values empirically for the specific system to be simulated.

    The method "screened" uses the real-space part of the Ewald sum with a charge-neutralizing surface charge density around the cutoff sphere, and no reciprocal sum [Wolf1999]. It requires the specification of the dictionary entries "cutoff" and "beta".

    The fast-multipole method uses the DPMTA library [DPMTA]. Note that this method provides only energy and forces, but no second-derivative matrix. There are several optional dictionary entries for this method, all of which are set to reasonable default values. The entries are "spatial_decomposition_levels", "multipole_expansion_terms", "use_fft", "fft_blocking_factor", "macroscopic_expansion_terms", and "multipole_acceptance". For an explanation of these options, refer to the DPMTA manual [DPMTA].