Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber.
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 multi-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.
Luchko
Tyler
T
National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada.
Gusarov
Sergey
S
Roe
Daniel R
DR
Simmerling
Carlos
C
Case
David A
DA
Tuszynski
Jack
J
Kovalenko
Andriy
A