The QM-MM interface for CHARMM-deMon.
We present a new QM/MM interface for fast and efficient simulations of organic and biological molecules. The CHARMM/deMon interface has been developed and tested to perform minimization and atomistic simulations for multi-particle systems. The current features of this QM/MM interface include readability for molecular dynamics, tested compatibility with Free Energy Perturbation simulations (FEP) using the dual topology/single coordinate method. The current coupling scheme uses link atoms, but further extensions of the code to incorporate other available schemes are planned. We report the performance of different levels of theory for the treatment of the QM region, while the MM region was represented by a classical force-field (CHARMM27) or a polarizable force-field based on a simple Drude model. The current QM/MM implementation can be coupled to the dual-thermostat method and the VV2 integrator to run molecular dynamics simulations.
Lev
Bogdan
B
Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4.
Zhang
Rui
R
de la Lande
Aurélien
A
Salahub
Dennis
D
Noskov
Sergei Yu
SY
D019281:Dimerization; D056004:Molecular Dynamics Simulation; D011188:Potassium / Q000737:chemistry; D011789:Quantum Theory; D012964:Sodium / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D014867:Water; D012964:Sodium; D011188:Potassium