Premium
Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins
Author(s) -
Gelpí Josep Lluis,
Kalko Susana G.,
Barril Xavier,
Cirera Jordi,
de la Cruz Xavier,
Luque F. Javier,
Orozco Modesto
Publication year - 2001
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.1159
Subject(s) - molecular dynamics , process (computing) , computer science , counterion , chemistry , ion , statistical physics , computational chemistry , physics , organic chemistry , operating system
The latest version of the classical molecular interaction potential (CMIP) has the ability to predict the position of crystallographic waters in several proteins with great accuracy. This article analyzes the ability of the CMIP functional to improve the setup procedure of the molecular system in molecular dynamics (MD) simulations of proteins. To this end, the CMIP strategy is used to include both water molecules and counterions in different protein systems. The structural details of the configurations sampled from trajectories obtained using the CMIP setup procedure are compared with those obtained from trajectories derived from a standard equilibration process. The results show that standard MD simulations can lead to artifactual results, which are avoided using the CMIP setup procedure. Because the CMIP is easy to implement at a low computational cost, it can be very useful in obtaining reliable MD trajectories. Proteins 2001;45:428–437. © 2001 Wiley‐Liss, Inc.