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Items: 1 to 20 of 101

1.

Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems.

Fass J, Sivak DA, Crooks GE, Beauchamp KA, Leimkuhler B, Chodera JD.

Entropy (Basel). 2018 May;20(5). pii: 318. doi: 10.3390/e20050318. Epub 2018 Apr 26.

2.

Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems.

Sivak DA, Chodera JD, Crooks GE.

J Phys Chem B. 2014 Jun 19;118(24):6466-74. doi: 10.1021/jp411770f. Epub 2014 Mar 17.

3.

New Langevin and gradient thermostats for rigid body dynamics.

Davidchack RL, Ouldridge TE, Tretyakov MV.

J Chem Phys. 2015 Apr 14;142(14):144114. doi: 10.1063/1.4916312.

4.

Unbiased reduced density matrices and electronic properties from full configuration interaction quantum Monte Carlo.

Overy C, Booth GH, Blunt NS, Shepherd JJ, Cleland D, Alavi A.

J Chem Phys. 2014 Dec 28;141(24):244117. doi: 10.1063/1.4904313.

PMID:
25554143
5.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug 2;10(4):040301. [Epub ahead of print]

PMID:
23912807
6.

Long timestep dynamics of peptides by the dynamics driver approach.

Derreumaux P, Schlick T.

Proteins. 1995 Apr;21(4):282-302.

PMID:
7567951
7.

Numerical integration of the extended variable generalized Langevin equation with a positive Prony representable memory kernel.

Baczewski AD, Bond SD.

J Chem Phys. 2013 Jul 28;139(4):044107. doi: 10.1063/1.4815917.

PMID:
23901960
8.

Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements.

Gore J, Ritort F, Bustamante C.

Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12564-9. Epub 2003 Oct 3.

9.

Robust and efficient configurational molecular sampling via Langevin dynamics.

Leimkuhler B, Matthews C.

J Chem Phys. 2013 May 7;138(17):174102. doi: 10.1063/1.4802990.

PMID:
23656109
10.

Simulating rare events in equilibrium or nonequilibrium stochastic systems.

Allen RJ, Frenkel D, ten Wolde PR.

J Chem Phys. 2006 Jan 14;124(2):024102.

PMID:
16422566
11.

On the effect of the thermostat in non-equilibrium molecular dynamics simulations.

Ruiz-Franco J, Rovigatti L, Zaccarelli E.

Eur Phys J E Soft Matter. 2018 Jul 2;41(7):80. doi: 10.1140/epje/i2018-11689-4.

PMID:
29955976
12.
13.

Adaptive Splitting Integrators for Enhancing Sampling Efficiency of Modified Hamiltonian Monte Carlo Methods in Molecular Simulation.

Akhmatskaya E, Fernández-Pendás M, Radivojević T, Sanz-Serna JM.

Langmuir. 2017 Oct 24;33(42):11530-11542. doi: 10.1021/acs.langmuir.7b01372. Epub 2017 Aug 2.

PMID:
28689416
14.

Metadynamics convergence law in a multidimensional system.

Crespo Y, Marinelli F, Pietrucci F, Laio A.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 May;81(5 Pt 2):055701. Epub 2010 May 7.

PMID:
20866290
15.

A path-integral Langevin equation treatment of low-temperature doped helium clusters.

Ing C, Hinsen K, Yang J, Zeng T, Li H, Roy PN.

J Chem Phys. 2012 Jun 14;136(22):224309. doi: 10.1063/1.4726507.

PMID:
22713049
16.

Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules.

Hédin F, Plattner N, Doll JD, Meuwly M.

J Chem Theory Comput. 2014 Oct 14;10(10):4284-96. doi: 10.1021/ct500529w.

PMID:
26588125
17.

Assessing numerical methods for molecular and particle simulation.

Shang X, Kröger M, Leimkuhler B.

Soft Matter. 2017 Nov 22;13(45):8565-8578. doi: 10.1039/c7sm01526g.

PMID:
29099134
18.

Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.

Cooke B, Schmidler SC.

J Chem Phys. 2008 Oct 28;129(16):164112. doi: 10.1063/1.2989802.

PMID:
19045252
19.

Path integral Monte Carlo with importance sampling for excitons interacting with an arbitrary phonon bath.

Shim S, Aspuru-Guzik A.

J Chem Phys. 2012 Dec 14;137(22):22A538. doi: 10.1063/1.4751487.

PMID:
23249075
20.

Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms.

Barash D, Yang L, Qian X, Schlick T.

J Comput Chem. 2003 Jan 15;24(1):77-88.

PMID:
12483677

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