Abstract
An algorithm is presented for the simulation of two partially flexible macromolecules where the interaction between the flexible parts and rigid parts is represented by energy grids associated with the rigid part of each macromolecule. The proposed algorithm avoids the transformation of the grid upon molecular movement at the expense of the significantly lesser effect of transforming the flexible part.
Highlights
Atomic level simulation of macromolecules is currently performed almost exclusively by molecular dynamics
A further advantage of the Monte Carlo approach over molecular dynamics is the ease of limiting the sampling to certain parts of the system and/or to a limited set of degrees of freedom
This idea has been combined with the Monte Carlo approach for the simulation of protein loops [7] where only a small part of the molecule is moved during the simulation, achieving similar speedup
Summary
Atomic level simulation of macromolecules is currently performed almost exclusively by molecular dynamics. Since the most likely macromolecule type to be modeled is a protein and protein domains have well over a thousand atoms (i.e., NR ' 1000 is a low estimate in most cases), using the grid representation saves a factor of NR /10, that is, likely a factor of ~100 or more This idea has been combined with the Monte Carlo approach for the simulation of protein loops [7] where only a small part of the molecule is moved during the simulation, achieving similar speedup. When modeling the interaction of two partially rigid macromolecules, the straightforward extension of these algorithms would run into the difficulty of having to move at least one of the sets of grids This introduces additional computation expenses: (a) finding the nearest eight gridpoints. This note describes an algorithm that allows the movement of the rigid part while maintaining
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
