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Gemini Computing Cluster | Department of Biochemistry and Molecular Biology

The Gemini Computing Cluster is a state of the art high performance computing cluster, leveraging modern technologies such as GPU computing. The Schrödinger suite of software applications provides researchers with the tools needed for performing advanced analysis of biological molecules. Custom versions of the Amber 14 Molecular Dynamics package enable rapid sampling of macromolecular conformations. Quick Facts About Gemini. 72 TFLOPs peak computing power. 64 GB RAM/node (1.3 TB aggregate). Sequence sele...

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Gemini Computing Cluster | Department of Biochemistry and Molecular Biology | geminiweb.slu.edu Reviews

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The Gemini Computing Cluster is a state of the art high performance computing cluster, leveraging modern technologies such as GPU computing. The Schrödinger suite of software applications provides researchers with the tools needed for performing advanced analysis of biological molecules. Custom versions of the Amber 14 Molecular Dynamics package enable rapid sampling of macromolecular conformations. Quick Facts About Gemini. 72 TFLOPs peak computing power. 64 GB RAM/node (1.3 TB aggregate). Sequence sele...

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2 cluster hardware

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4 publications and funding

5 software

6 resources and help

7 amber

8 compilers

9 job submission

10 modules

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Gemini Computing Cluster | Department of Biochemistry and Molecular Biology | geminiweb.slu.edu Reviews

https://geminiweb.slu.edu

The Gemini Computing Cluster is a state of the art high performance computing cluster, leveraging modern technologies such as GPU computing. The Schrödinger suite of software applications provides researchers with the tools needed for performing advanced analysis of biological molecules. Custom versions of the Amber 14 Molecular Dynamics package enable rapid sampling of macromolecular conformations. Quick Facts About Gemini. 72 TFLOPs peak computing power. 64 GB RAM/node (1.3 TB aggregate). Sequence sele...

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geminiweb.slu.edu

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Crystal structure of prothrombin reveals conformational flexibility and mechanism of activation | Gemini Computing Cluster

http://geminiweb.slu.edu/crystal-structure-of-prothrombin-reveals-conformational-flexibility-and-mechanism-of-activation

Crystal structure of prothrombin reveals conformational flexibility and mechanism of activation. August 1, 2013. March 8, 2015. Pozzi N, Chen Z, Gohara DW, Niu W, Heyduk T, Di Cera E. J Biol. Chem. 2013 Aug;288(31):22734-44. Routine Access to Millisecond Time…. Twenty-five years of nucleic acid… →. Department of Biochemistry and Molecular Biology. Saint Louis University School of Medicine. Department of Biochemistry and Molecular Biology. Saint Louis University School of Medicine. 1100 South Grand Blvd.

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Software | Gemini Computing Cluster

http://geminiweb.slu.edu/software

March 7, 2015. March 8, 2015. Biologics, Molecular Dynamics and Small Molecule Docking. AMBER (Assisted Model Building with Energy Refinement) is a set of molecular mechanical force fields for the simulation of biomolecules and a package of molecular simulation programs which includes source code and demos. Installed versions include Amber 12 and 14. The Schrodinger software suite consists of a number of applications comprised of small-molecule lead discovery and optimization, quantum mechanics, homology...

3

Publications and Funding | Gemini Computing Cluster

http://geminiweb.slu.edu/publications-and-funding

March 7, 2015. March 8, 2015. Development and Application of the AMOEBA Polarizable Force Field. National Science Foundation. Aug 2012 - Jul 2015. Award Number: 1152522. RNA-dependent RNA polymerase. National Institutes of Health. (PI: Craig Cameron, Subcontract: David Gohara). Funded Projects That Utilized the Cluster. Ligand- and sequence-specific inhibition of protein synthesis by antibiotics. Edward J. Mallinckrodt Foundation. (PI: Frances Yap). February 24, 2015. March 8, 2015. December 26, 2014.

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Amber | Gemini Computing Cluster

http://geminiweb.slu.edu/resources-and-help/amber

March 7, 2015. March 8, 2015. Amber Molecular Dynamics Package. There are several versions of the Amber MD package available on Gemini. The older Amber 12 is still available, but in general should not be used. Amber 14, the current version is the preferred version. In addition to the standard Amber build (including AmberTools), there are versions of the main MD programs (sander and pmemd) that work under MPI, CUDA and CUDA MPI. Module load amber/amber14 ramddb. Sbatch -n 32 mpirun pmemd.MPI -O -i mdi...

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Schrödinger Suite | Gemini Computing Cluster

http://geminiweb.slu.edu/resources-and-help/schrodinger-suite

March 7, 2015. March 9, 2015. The Schrodinger suite of software has a large number of applications for a variety modeling, analysis and computational tasks. In general the program is run on your local computer and there are installers for OS X, Linux and Windows. In addition to running locally many if not all of the programs can be run on the cluster using the job submission utilities within the suite. To get a copy of the program installers contact David Gohara. Chimeric and multimeric models. Advanced ...

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biochem.slu.edu

Edward A. Doisy Department of Biochemistry and Molecular Biology

http://biochem.slu.edu/index.shtml

Edward A. Doisy Department of. Biochemistry and Molecular Biology. 193;ngel Baldán. David A. Ford. Alireza R. Rezaie. William S. Sly. David Q.H. Wang. Graduate and Medical Programs. NIH Contract Funds 'Omics Research. Several faculty will participate on an NIH contract a contract to study the safety and efficacy. Of vaccines using "omics" research techniques to determine how the immune system. Faculty Receive Collaborative Grants. William S. Sly Fellowship in Biomedical Sciences. Completed in 2007, the E...

biochemweb.slu.edu

Edward A. Doisy Department of Biochemistry and Molecular Biology

http://biochemweb.slu.edu/index.shtml

Edward A. Doisy Department of. Biochemistry and Molecular Biology. 193;ngel Baldán. David A. Ford. Alireza R. Rezaie. William S. Sly. David Q.H. Wang. Graduate and Medical Programs. NIH Contract Funds 'Omics Research. Several faculty will participate on an NIH contract a contract to study the safety and efficacy. Of vaccines using "omics" research techniques to determine how the immune system. Faculty Receive Collaborative Grants. William S. Sly Fellowship in Biomedical Sciences. Completed in 2007, the E...

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geminiweb.slu.edu

Gemini Computing Cluster | Department of Biochemistry and Molecular Biology

The Gemini Computing Cluster is a state of the art high performance computing cluster, leveraging modern technologies such as GPU computing. The Schrödinger suite of software applications provides researchers with the tools needed for performing advanced analysis of biological molecules. Custom versions of the Amber 14 Molecular Dynamics package enable rapid sampling of macromolecular conformations. Quick Facts About Gemini. 72 TFLOPs peak computing power. 64 GB RAM/node (1.3 TB aggregate). Sequence sele...

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