ELECTROSTATICS AND DIFFUSION OF MOLECULES IN SOLUTION - SIMULATIONS WITH THE UNIVERSITY-OF-HOUSTON BROWNIAN DYNAMICS PROGRAM

Authors
MADURA JD BRIGGS JM WADE RC DAVIS ME LUTY BA ILIN A ANTOSIEWICZ J GILSON MK BAGHERI B SCOTT LR MCCAMMON JA
Citation
Jd. Madura et al., ELECTROSTATICS AND DIFFUSION OF MOLECULES IN SOLUTION - SIMULATIONS WITH THE UNIVERSITY-OF-HOUSTON BROWNIAN DYNAMICS PROGRAM, Computer physics communications, 91(1-3), 1995, pp. 57-95
Citations number
87
Categorie Soggetti
Mathematical Method, Physical Science","Physycs, Mathematical","Computer Science Interdisciplinary Applications
Journal title
Computer physics communications → ACNP
ISSN journal
00104655
Volume
91
Issue
1-3
Year of publication
1995
Pages
57 - 95
Database
ISI
SICI code
0010-4655(1995)91:1-3<57:EADOMI>2.0.ZU;2-K
Abstract
This paper is a follow-up to the initial communication (Comput. Phys. Commun. 62 (1991) 187-197) on the Brownian Dynamics/Electrostatics pro gram UHBD developed at the University of Houston. The program is now c apable of computing pK(a)s of ionizable groups in proteins, performing Brownian dynamics simulations with a flexible substrate and target, a nd molecular mechanics/dynamics calculations using a continuum solvent . These new capabilities and other features are discussed along with s elected applications which illustrate the capabilities of the current version of UHBD.