Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 8, Issue 1, Pages 17-23Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct200615k
Keywords
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Funding
- Molecular Biophysics Training Grant [GM08326]
- National Science Foundation [MCB-0506593]
- NBCR
- CTBP
- Howard Hughes Medical Institute
- National Institutes of Health [GM31749]
- Direct For Biological Sciences
- Div Of Molecular and Cellular Bioscience [1020765] Funding Source: National Science Foundation
- Division Of Physics
- Direct For Mathematical & Physical Scien [1308264] Funding Source: National Science Foundation
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Molecular dynamics (MD) is one of the most common tools in computational chemistry. Recently, our group has employed accelerated molecular dynamics (aMD) to improve the conformational sampling over conventional molecular dynamics techniques. In the original aMD implementation, sampling is greatly improved by raising energy wells below a predefined energy level. Recently, our group presented an alternative aMD implementation where simulations are accelerated by lowering energy barriers of the potential energy surface. When coupled with thermodynamic integration simulations, this implementation showed very promising results. However, when applied to large systems, such as proteins, the simulation tends to be biased to high energy regions of the potential landscape. The reason for this behavior lies in the boost equation used since the highest energy barriers are dramatically more affected than the lower ones. To address this issue, in this work, we present a new boost equation that prevents oversampling of unfavorable high energy conformational states. The new boost potential provides not only better recovery of statistics throughout the simulation but also enhanced sampling of statistically relevant regions in explicit solvent MD simulations.
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