PUPIL: a software integration system for multi-scale QM/MM-MD simulations and its application to biomolecular systems
10.1016/bs.apcsb.2015.06.002
Inclou dades d'ús des de 2022
Cita com:
hdl:2117/78164
Tipus de documentArticle
Data publicació2015-07-04
Condicions d'accésAccés obert
Tots els drets reservats. Aquesta obra està protegida pels drets de propietat intel·lectual i
industrial corresponents. Sense perjudici de les exempcions legals existents, queda prohibida la seva
reproducció, distribució, comunicació pública o transformació sense l'autorització del titular dels drets
Abstract
PUPIL (Program for User Package Interfacing and Linking) implements a distinctive multi-scale approach to hybrid quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations. Originally developed to interface different external programs for multi-scale simulation with applications in the materials sciences, PUPIL is finding increasing use in the study of complex biological systems. Advanced MD techniques from the external packages can be applied readily to a hybrid QM/MM treatment in which the forces and energy for the QM region can be computed by any of the QM methods available in any of the other external packages. Here, we give a survey of PUPIL design philosophy, main features, and key implementation decisions, with an orientation to biomolecular simulation. We discuss recently implemented features which enable highly realistic simulations of complex biological systems which have more than one active site that must be treated concurrently. Examples are given
CitacióTorras, J., Roberts, B.P., Seabra, G.M., Trickey, S.B. PUPIL: a software integration system for multi-scale QM/MM-MD simulations and its application to biomolecular systems. "Advances in Protein Chemistry and Structural Biology", 04 Juliol 2015, vol. 100, p. 1-31.
ISSN1876-1623
Versió de l'editorhttp://dx.doi.org/10.1016/bs.apcsb.2015.06.002
Fitxers | Descripció | Mida | Format | Visualitza |
---|---|---|---|---|
Pupil_asoftware.pdf | 307,8Kb | Visualitza/Obre | ||
Pupil_asoftware.pdf | 307,8Kb | Visualitza/Obre |