Calculation of the potential of mean force using molecular dynamics with linear constraints: An application to a conformational transition in a solvated dipeptide
10.1063/1.458713
Crossref journal-article
AIP Publishing
The Journal of Chemical Physics (317)
Abstract

An algorithm is proposed for the calculation of mean force potentials using molecular dynamics with linear constraints. The new algorithm is based on free energy perturbation and is especially useful when the analytical form of the reaction coordinate is not known (e.g., for a numerically evaluated steepest descent path). It employs only Cartesian coordinates which makes it easy to use for a variety of systems. In particular, it is useful when the reaction coordinate cannot be represented by a single local coordinate or by a combination of a small number of local (internal) coordinates. The linear constraints are solved explicitly and the computational effort required is similar to that of dynamics with no constraints. The potential of mean force for a conformational transition of a solvated valine dipeptide is calculated. In aqueous solution the barriers for the conformational transitions are reduced with respect to the barriers in vacuo, the helix configuration becomes stabilized.

Bibliography

Elber, R. (1990). Calculation of the potential of mean force using molecular dynamics with linear constraints: An application to a conformational transition in a solvated dipeptide. The Journal of Chemical Physics, 93(6), 4312–4321.

Authors 1
  1. Ron Elber (first)
References 37 Referenced 59
  1. 10.1021/ja00390a043 / J. Am. Chem. Soc. (1982)
  2. 10.1063/1.443732 / J. Chem. Phys. (1982)
  3. 10.1073/pnas.79.13.4035 / Proc. Natl. Acad. Sci. US (1982)
  4. 10.1021/ja00287a028 / J. Am. Chem. Soc. (1985)
  5. 10.1021/ja00296a024 / J. Am. Chem. Soc. (1985)
  6. 10.1021/ja00294a005 / J. Am. Chem. Soc. (1985)
  7. 10.1021/j100283a001 / J. Phys. Chem. (1986)
  8. 10.1111/j.1749-6632.1986.tb20953.x / Proc. N. Y. Acad. Sci. (1986)
  9. 10.1021/ja00241a001 / J. Am. Chem. Soc. (1987)
  10. 10.1021/j100308a003 / J. Phys. Chem. (1987)
  11. 10.1021/ja00252a042 / J. Am. Chem. Soc. (1987)
  12. 10.1021/ja00229a010 / J. Am. Chem. Soc. (1988)
  13. 10.1021/ja00231a018 / J. Am. Chem. Soc. (1988)
  14. {'key': '2024021010143000700_r13', 'first-page': '362', 'volume': '3', 'year': '1988', 'journal-title': 'Proteins'} / Proteins (1988)
  15. 10.1016/0009-2614(87)80646-2 / Chem. Phys. Lett. (1987)
  16. 10.1063/1.455654 / J. Chem. Phys. (1988)
  17. 10.1063/1.456651 / J. Chem. Phys. (1989)
  18. 10.1016/0009-2614(89)85222-4 / Chem. Phys. Lett. (1989)
  19. 10.1021/ja00158a005 / J. Am. Chem. Soc. (1990)
  20. 10.1002/prot.340070308 / Proteins (1990)
  21. {'key': '2024021010143000700_r19'}
  22. 10.1016/0009-2614(87)80576-6 / Chem. Phys. Lett. (1987)
  23. 10.1073/pnas.86.18.6963 / Proc. Natl. Acad. Sci. US (1989)
  24. 10.1063/1.458112 / J. Chem. Phys. (1990)
  25. 10.1063/1.458491 / J. Chem. Phys. (1990)
  26. {'key': '2024021010143000700_r20d'}
  27. {'key': '2024021010143000700_r20e'}
  28. {'key': '2024021010143000700_r20f'}
  29. 10.1063/1.446137 / J. Chem. Phys. (1983)
  30. 10.1016/0021-9991(77)90098-5 / J. Comput. Phys. (1977)
  31. 10.1016/0021-9991(89)90160-5 / J. Comput. Phys. (1989)
  32. {'key': '2024021010143000700_r24'}
  33. {'key': '2024021010143000700_r25'}
  34. 10.1063/1.440496 / J. Chem. Phys. (1980)
  35. 10.1063/1.441213 / J. Chem. Phys. (1981)
  36. 10.1002/jcc.540040211 / J. Comput. Chem. (1983)
  37. 10.1063/1.445869 / J. Chem. Phys. (1983)
Dates
Type When
Created 23 years ago (July 26, 2002, 9:14 a.m.)
Deposited 1 year, 6 months ago (Feb. 10, 2024, 7:04 a.m.)
Indexed 4 months, 1 week ago (April 17, 2025, 7:04 p.m.)
Issued 34 years, 11 months ago (Sept. 15, 1990)
Published 34 years, 11 months ago (Sept. 15, 1990)
Published Print 34 years, 11 months ago (Sept. 15, 1990)
Funders 0

None

@article{Elber_1990, title={Calculation of the potential of mean force using molecular dynamics with linear constraints: An application to a conformational transition in a solvated dipeptide}, volume={93}, ISSN={1089-7690}, url={http://dx.doi.org/10.1063/1.458713}, DOI={10.1063/1.458713}, number={6}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Elber, Ron}, year={1990}, month=sep, pages={4312–4321} }