Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent

Journal of Chemical Physics

Volumn 135, Issue 15, 2011, Pages

  Wu, Johnny ^a   Zhen, Xia ^a   Shen, Hujun ^b   Li, Guohui ^b   Ren, Pengyu ^a  

^a The University of Texas at Austin   (United States)

^b DALIAN INSTITUTE OF CHEMICAL PHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE DIPEPTIDES; ALL-ATOM FORCE FIELD; ALL-ATOM SIMULATIONS; ALPHA HELIX; ATOMIC MODELS; BETA-SHEET; BETA-STRAND; BIO-MOLECULAR; COARSE GRAINING; CONFORMATIONAL DISTRIBUTION; CONFORMATIONAL ENERGIES; EFFECTIVE FORCES; GAY-BERNE; GAY-BERNE POTENTIALS; IMPLICIT SOLVENTS; INTERMOLECULAR FORCES; MICROSECOND DYNAMICS; MODEL COMPOUND; MULTIPOLE EXPANSIONS; MULTIPOLES; POLYALANINE; POLYPEPTIDE SIMULATIONS; REPLICA EXCHANGE MOLECULAR DYNAMICS; SOLUTION PHASIS; SOLVENT EFFECTS;

AMINO ACIDS; ATOMS; CHEMICAL BONDS; ELECTRON ENERGY LEVELS; ELECTROSTATICS; MOLECULAR DYNAMICS; POLYPEPTIDES; SOLVATION;

COMPUTER SIMULATION;

ALANYLALANINE; DIPEPTIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; STATIC ELECTRICITY; THERMODYNAMICS;

COMPUTER SIMULATION; DIPEPTIDES; MODELS, MOLECULAR; MOLECULAR CONFORMATION; STATIC ELECTRICITY; THERMODYNAMICS;

EID: 80155157254     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3651626     Document Type: Article

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49. See supplementary material at http://dx.doi.org/10.1063/1.3651626 E-JCPSA6-135-040139 for following details: Table S1: Gay-Berne parameters of benzene, methanol, and water GBEMP models; Table S2: MD simulation results for benzene; Table S3: MD simulation results for methanol; Table S4: Bond, bond-angle, torsional, and multiple parameters for GBEMP model. Table S5: Comparison of computational efficiency of GBEMP model with all-atom simulations. Figure S1: comparison of homodimer interaction energy give by the Gay-Berne model and all-atom model for benzene and methanol; Figure S2: phi and psi torsion angle distribution of 12-mer polyalanine at temperature of 800 K to 900 K in the simulated annealing simulation; Figure S3: phi and psi torsion angle distribution of 12-mer polyalanine at temperature of 1 K to 100 K in the simulated annealing simulation; Figure S4: contribution of torsional energy to total conformational energy of dialanine GBEMP model and All-atom OPLSAA; Figure S5: Simulated annealing MD simulations to inspect the minimum-energy structure of the peptide after an initial rigid-body energy minimization. (a) A final snapshot of polyalanine from the 60-ns simulated annealing simulations using GBEMP potential. (b) Heavy-atom RMSD of the 12-residue polyalanine from 5 simulated annealing simulations; Figure S6: conformational distributions of 5-mer and 12-mer polyalanine from CG simulations at 298 K.