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Torsional potential for “butanelike” molecule used as model system. Solid line represents unscaled potential for this butanelike molecule; dash line represents scaled potential potential . Exchange occurring when replicas are in the same conformational region as unproductive one for canonical sampling, while one occurring when replicas are in the different conformational region is productive exchange.
Efficiency comparison between FRREM and REM in “butanelike” model system. (a) Dihedral angle changes as function of simulation time. (b) Time evolution of ratio of cumulative distribution of dihedral angle in the range (0, 180). (c) Time evolution of standard deviation for ratio of cumulative distribution of dihedral angle in the range (0,180). The results from FRREM are labeled by open circle and dotted line and those from REM are labeled by solid circle and solid line.
Suggested designs for FRREM simulation. (a) Finite reservoir is set in the middle of two “temperature” runs. (b) Flexible combination of finite reservoirs with real time simulations.
Time evolution of computed potential of mean forces around leucine angle using three different sampling methods. (a) Using regular REM. (b) Using one CPU FRREM. (c) Using two-CPU FRREM. Potential of mean forces were computed based on occurrence probability in the simulations on unscaled potential.
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