期刊
JOURNAL OF CHEMICAL PHYSICS
卷 133, 期 8, 页码 -出版社
AMER INST PHYSICS
DOI: 10.1063/1.3478526
关键词
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资金
- NSF [CHE0748628]
- HP outstanding Junior Faculty
- National Center for Supercomputing Applications [MRAC TG-CHE070060]
- Boston University Center for Scientific Computing
The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3478526]
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