Polymer dynamics in torsion space.
J Comput Chem
; 31(9): 1882-8, 2010 Jul 15.
Article
em En
| MEDLINE
| ID: mdl-20058226
ABSTRACT
The large scale motion of proteins, or covalently bonded polymers in general, is governed by the dynamics of the torsion angles, with bond lengths and bond angles kept approximately constant. In the present work, the Lagrangian equations of torsion motion are derived for a general macromolecule. The dynamics is implemented numerically for a test protein, using the velocity Verlet method as the integrator. The results indicate time steps of up to about 30 fs can be used for short time (up to at least 20 ps) simulations, before the dynamics and energy start to differ significantly from results obtained with smaller time steps. For longer time simulations, up to 1000 ps, a time step of 10 fs is relatively safe.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Polímeros
/
Proteínas
/
Modelos Químicos
Idioma:
En
Ano de publicação:
2010
Tipo de documento:
Article