Paper Citing NAMD - Abstract
Ufimtsev, Ivan S.; Luehr, Nathan; Martinez, Todd J.
Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:1789-1793, JUL 21 2011
Charge transfer at the Bovine pancreatic trypsin inhibitor (BPTI) protein-water interface was analyzed by means of ab initio Born-Oppenheimer molecular dynamics simulation of the entire protein running on graphical processing units (GPUs). The efficiency of the GPU-based quantum chemistry algorithms implemented in our TeraChem program enables us to perform these calculations on a desktop computer. Mulliken and Voronoi deformation density (VDD) population analysis reveals that between 2.0 and 3.5 electrons are transferred from surrounding water molecules to the protein over the course of the 8.8 Ps simulation. Solving for the electronic structure of BPTI in the absence of surrounding water molecules (i.e., in the gas phase) leads to large intraprotein charge transfer, where approximately one electron in total is transferred from neutral to polar residues. Solvation relieves this polarization stress, leading to a neutralization of the excess positive charge of the neutral residues.
