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Multiple scaling replica exchange for the conformational sampling of biomolecules in explicit water
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Image of FIG. 1.
FIG. 1.

(a) The probability distributions of potential energy (in kcal/mol), for the standard MD simulations, (b) of the potential energy term, for REST, (c) of the generalized effective potential for MREST, and (d) of the potential energy term, for MREST-DIHE at different values of the temperature and/or scaling factor .

Image of FIG. 2.
FIG. 2.

The probability distributions of the energy term at different replica runs for the MREST method.

Image of FIG. 3.
FIG. 3.

The RMSD variance between two independent trajectories [see Eq. (16)] as a function of the simulation time. The data from all replicas are used to construct the histograms of the RMSD.

Image of FIG. 4.
FIG. 4.

Fractions of replicas visiting the lowest and the highest temperatures in the MREST-DIHE, MREST, and REST methods of simulations.

Image of FIG. 5.
FIG. 5.

(Color online) Free energy contour map vs the backbone dihedral angles ( and ) of the peptide from REST (top), MREST (middle), and MREST-DIHE (bottom) methods, weighted at the temperature and collected for 0.3, 0.75, and , as depicted in figure. The contours are spaced at intervals of . The energy scale is in kcal/mol. The white regions denote areas not visited during the course of simulations.


Generic image for table
Table I.

Overlap probability of the energy distribution between two neighboring replicas calculated as the surface area of overlap between the two energy distribution curves: for REST method, for MREST, and for MREST-DIHE, of the replicas and .


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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Multiple scaling replica exchange for the conformational sampling of biomolecules in explicit water