Locally enhanced sampling (LES) [57,61,62] increases sampling and transition rates for a portion of a molecule by the use of multiple non-interacting copies of the enhanced atoms. These enhanced atoms experience an interaction (electrostatics, van der Waals, and covalent) potential that is divided by the number of copies present. In this way the enhanced atoms can occupy the same space, while the multiple instances and reduces barriers increase transition rates.
To use LES, the structure and coordinate input files must be modified to contain multiple copies of the enhanced atoms. psfgen provides the multiply command for this purpose. NAMD supports a maximum of 255 copies, which should be sufficient.
Begin by generating the complete molecular structure and guessing
coordinates as described in Sec. 4. As the last
operation in your script, prior to writing the psf and pdb files, add
the multiply command, specifying the number of copies desired and
listing segments, residues, or atoms to be multiplied. For example,
multiply 4 BPTI:56 BPTI:57 will create four copies of the last
two residues of segment BPTI. You must include all atoms to be
enhanced in a single multiply command in order for the bonded
terms in the psf file to be duplicated correctly. Calling multiply
on connected sets of atoms multiple times will produce unpredictable
results, as may running other commands after multiply.
The enhanced atoms are duplicated exactly in the structure--they have
the same segment, residue, and atom names. They are distinguished only
by the value of the B (beta) column in the pdb file, which is 0 for
normal atoms and varies from 1 to the number of copies created for
enhanced atoms. The enhanced atoms may be easily observed in VMD with
the atom selection
beta != 0.
In practice, LES is a simple method used to increase sampling; no special output is generated. The following parameters are used to enable LES:
number of LES images to use
Acceptable Values: positive integer equal to the number of images present
Description: This should be equal to the factor used in multiply when creating the structure. The interaction potentials for images is divided by lesFactor.