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Subsections


Locally enhanced sampling

Locally enhanced sampling (LES) [60,64,65] 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.

Structure generation

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.

Simulation

In practice, LES is a simple method used to increase sampling; no special output is generated. The following parameters are used to enable LES:


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Next: Replica exchange simulations Up: Accelerated Sampling Methods Previous: Adaptive Tempering   Contents   Index
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