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CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals,(More)
A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with Hartree-Fock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capability has been implemented in the CHARMM and Q-Chem software packages. In addition, we have modified CHARMM and Q-Chem to take advantage of the newly introduced replica path and the nudged(More)
A new web portal for the CHARMM macromolecular modeling package, CHARMMing (CHARMM interface and graphics, http://www.charmming.org), is presented. This tool provides a user-friendly interface for the preparation, submission, monitoring, and visualization of molecular simulations (i.e., energy minimization, solvation, and dynamics). The infrastructure used(More)
CROW (Columns and Rows Of Workstations - http://www.sicmm.org/crow/) is a parallel computer cluster based on the Beowulf (http://www.beowulf.org/) idea, modified to support a larger number of processors. Its architecture is based on point-to-point network architecture, which does not require the use of any network switching equipment in the system. Thus,(More)
In this article a procedure is derived to obtain a performance gain for molecular dynamics (MD) simulations on existing parallel clusters. Parallel clusters use a wide array of interconnection technologies to connect multiple processors together, often at different speeds, such as multiple processor computers and networking. It is demonstrated how to(More)
A force field of the triclinic framework of AlPO(4)-34, important in methanol-hydrocarbon conversion reactions, was developed using an empirical potential function. Molecular dynamics simulation of an AlPO(4)-34 triclinic framework segment of 1216 atoms, containing the template molecules isopropylamine and water, was performed with explicit consideration of(More)
The netropsin molecule preferentially binds to the four consecutive A.T base pairs of the DNA minor groove and could therefore inhibit the expression of specific genes. The understanding of its binding on a molecular level is indispensable for computer-aided design of new antitumor agents. This knowledge could be obtained via molecular dynamics (MD) and(More)
A number of inexpensive computers were benchmarked with the ab initio program Gaussian 94, using both small standard test jobs and larger density functional (DFT) calculations. Several varieties of Pentium (x86) and Alpha CPU based systems were tested. Most of them were running under the open source code operating system Linux. They were compared with(More)
Thrombin is a serine protease which plays important roles in the human body, the key one being the control of thrombus formation. The inhibition of thrombin has become a target for new antithrombotics. The aim of our work was to (i) construct a model which would enable us to predict Ki values for the binding of an inhibitor into the active site of thrombin(More)
Prion diseases are fatal neurodegenerative diseases thought to arise from the post-translational conversion of normal cellular prion protein to a scrapie isoform. Experimental data suggest a role for copper(II) ions in the process. An ab initio QM/MM approach and available experimental data were combined in order to identify and evaluate three potential(More)