Mimicking coarse-grained simulations without coarse-graining: enhanced sampling by damping short-range interactions.
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.
Wei
Dongshan
D
Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.
Wang
Feng
F
D000465:Algorithms; D001704:Biopolymers / Q000737:chemistry*; D004134:Dimyristoylphosphatidylcholine / Q000737:chemistry; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D018716:Molecular Mimicry; D009584:Nitrogen / Q000737:chemistry; D010100:Oxygen / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D010758:Phosphorus / Q000737:chemistry; D017510:Protein Folding; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D001704:Biopolymers; D010455:Peptides; D014867:Water; D010758:Phosphorus; D009584:Nitrogen; D010100:Oxygen; D004134:Dimyristoylphosphatidylcholine