Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber
Journal Article
·
· Journal of Chemical Theory and Computation
We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multiple time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package and is illustrated here on alanine-dipeptide and protein-G.
- Research Organization:
- BROOKHAVEN NATIONAL LABORATORY (BNL)
- Sponsoring Organization:
- DOE - OFFICE OF SCIENCE
- DOE Contract Number:
- AC02-98CH10886
- OSTI ID:
- 1020830
- Report Number(s):
- BNL--91365-2010-JA; KJ0403000
- Journal Information:
- Journal of Chemical Theory and Computation, Journal Name: Journal of Chemical Theory and Computation Journal Issue: 3 Vol. 6; ISSN 1549-9618
- Country of Publication:
- United States
- Language:
- English
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