On the potential functions used in molecular dynamics simulations of ion channels [2]

Biophysical Journal

Volumn 82, Issue 3, 2002, Pages 1681-1684

  Roux, Benoît ^a   Bernèche, Simon ^a  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ION CHANNEL;

CALCULATION; CALIBRATION; ENERGY TRANSFER; ION PERMEABILITY; ION TRANSPORT; LETTER; MATHEMATICAL MODEL; MICROSCOPY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; SOLVATION; STRUCTURE ANALYSIS;

EID: 0036195868     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(02)75520-3     Document Type: Letter

References (30)

1. Molecular dynamics study of the KcsA potassium channel
2. Ion water interaction potential derived from free energy perturbation simulations
3. Ion permeation mechanism of the potassium channel
4. Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
5. Interaction models for water in relation to proteins hydration
6. Molecular dynamics of the KcsA K(+) channel in a bilayer membrane
7. + channel
8. Potassium and sodium ions in a potassium channel studied by molecular dynamics simulations
9. CHARMM: A program for macromolecular energy minimization and dynamics calculations
10. A second generation force field for the simulation of proteins and nucleic acids
11. Solvation of ions XIX. Thermodynamic properties for transfer of single ions between protic and dipolar aprotic solvents
12. + channels by TEA: Results from molecular dynamics simulations of the KcsA channel
13. A semi-microscopic Monte Carlo study of permeation energetics in a gramicidin-like channel: The origin of cation selectivity
14. The structure of the potassium channel: Molecular basis of K+ conduction and selectivity
15. n
16. Potassium and sodium binding to the outer mouth of the K+ channel
17. Polarizable force fields
18. Computer simulations of aqueous electrolyte solutions
19. A consistent empirical potential for water-protein interactions
20. Comparison of simple potential functions for simulating liquid water
21. Reaction enthalpies for M(+)L = M(+) + L, where M(+) = Na+ and K+ and L equals acetamide, N-methylacetamide, N,N-dimethylacetamide, glycine, and glycylglycine, from determinations of the collision-induced dissociation thresholds
22. K(+)/Na(+) selectivity of the KcsA potassium channel from microscopic free energy perturbation calculations
23. All-atom empirical potential for molecular modeling and dynamics studies of proteins
24. New values for the absolute solvation free energy of univalent ions in aqueous solution
25. + in the gramicidin channel
26. Potential energy function for cations-peptides interactions: An ab initio study
27. An empirical potential energy function for phospholipids: Criteria for parameters optimization and applications
28. Simulations of ion permeation through a potassium channel: Molecular dynamics of KcsA in a phospholipid bilayer
29. Improved simulation of liquid water by molecular dynamics
30. Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations