Unraveling Conformational Surfaces of Small Molecules Cont'd: Searching the Dihedral Angle Space

Important notice: This is a continuation project; please do not apply if you did not attend and finish the previous project last semester.
 
The free energy (FE) surface (Figure 1) with respect to one or more collective variables is proportional to -RTln[P], where P is the equilibrium probability distribution (PD) for a chemical system with respect to that specific collective variable.  Alas, obtaining an ergodic probability distribution for systems of increasing atomic count becomes increasingly impractical, so there have been many methods developed for approximating FE. in the first part of this project, students have determined that two different types of steered molecular dynamics (SMD) simulations yield two fair approximations of the real free energy surface at different domains – linear and quadratic.  The work is tentative, but our working hypothesis going forward is i) in the quadratic region, the slope of the approximated surface converges to the slope of the real surface as velocity is increased, and ii) in the linear region, the slope of the approximated surface converges to the slope of the real surface as velocity approaches zero.
 
In this continuation project, students will embed the execution of a new constant-torque force-finding algorithm into NAMD’s “calcforces” module so that constant torque simulations may be performed, for the elucidation of diethyl ether’s barrier characteristics. Such a force-finding algorithm may also enable low-velocity, single-fixed atom pulling simulations.