We describe a new interface of the GPU parallelized TeraChem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein...

We performed geometry optimizations using the tuned and balanced redistributed charge algorithms to treat the QM–MM boundary in combined quantum mechanical and molecular mechanical (QM/MM) methods. In the tuned and balanced redistributed charge (TBRC) scheme, the QM boundary atom is terminated by a tuned F link atom, and the charge of the MM boundary atom is properly adjusted to conserve the to...

A general procedure for quantum mechanics and molecular mechanics (QM/MM) studies on biochemical systems is outlined, and a collection of PERL scripts to facilitate ONIOM-type QM/MM calculations is described. This toolkit is designed to assist in the different stages of an ONIOM QM/MM study of biomolecules, including input file preparation and checking, job monitoring, production calculations, ...

We propose to demonstrate a practical alternative approach to the current state-of-the-art query processing techniques, called the “Query Mesh” (or QM, for short). The main idea of QM is to compute multiple routes (i.e., query plans), each designed for a particular subset of data with distinct statistical properties. Based on the execution routes and the data characteristics, a classifier model...

THE RELIABILITY OF FREE ENERGY SIMULATIONS (FES) IS LIMITED BY TWO FACTORS: (a) the need for correct sampling and (b) the accuracy of the computational method employed. Classical methods (e.g., force fields) are typically used for FES and present a myriad of challenges, with parametrization being a principle one. On the other hand, parameter-free quantum mechanical (QM) methods tend to be too c...

We performed geometry optimizations using the tuned and balanced redistributed charge algorithms to treat the QM-MM boundary in combined quantum mechanical and molecular mechanical (QM/MM) methods. In the tuned and balanced redistributed charge (TBRC) scheme, the QM boundary atom is terminated by a tuned F link atom, and the charge of the MM boundary atom is properly adjusted to conserve the to...

We have studied the convergence of QM/MM calculations with respect to the size of the QM system. We study a proton transfer between a first-sphere cysteine ligand and a second-sphere histidine group in [Ni,Fe] hydrogenase and use a 446-atom model of the protein, treated purely with QM methods as a reference. We have tested 12 different ways to redistribute charges close to the junctions (to avo...

We performed a comparative analysis of the arguments of Einstein, Podolsky and Rosen – EPR, 1935: [1] (against the completeness of QM) and the theoretical formalism of QM (due to von Neumann, 1932: [2]). We found that the EPR considerations do not match at all with the von Neumann's theory. Thus EPR did not criticize the real theoretical model of QM. The root of EPR's paradoxical conclusion on ...

Combined QM/MM calculations of an activesite of Cytochrome P450cam have been performed, before and after a binding process of Cytochrome P450cam to Putidaredoxin. The calculations have been carried out for two coordination spheres of the heme active-site of Cytochrome P450cam, namely a 5-coordinated, and a 6coordinated system of this protein having a water molecule as a 6th ligand. An experimen...