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Nikolay Simakov - Computational Modeling and Simulations

Computational Modeling and Simulations. This site is under construction. Center for Computational Research. University at Buffalo, SUNY. 701 Ellicott St., Buffalo, New York 14203. E-mail: nikolays@ccr.buffalo.edu. Below are several computational projects that I have been involved in. Is a toolkit developed by me to aid the molecular mechanical (MM) force field (FF) development for small drug-like molecule within the CHARMM/CGenFF Protocol. The work is done in Dr. Troy Wymore’s group. Olver) is GPU and CP...

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Nikolay Simakov - Computational Modeling and Simulations | compmodel.org Reviews
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Computational Modeling and Simulations. This site is under construction. Center for Computational Research. University at Buffalo, SUNY. 701 Ellicott St., Buffalo, New York 14203. E-mail: nikolays@ccr.buffalo.edu. Below are several computational projects that I have been involved in. Is a toolkit developed by me to aid the molecular mechanical (MM) force field (FF) development for small drug-like molecule within the CHARMM/CGenFF Protocol. The work is done in Dr. Troy Wymore’s group. Olver) is GPU and CP...
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Nikolay Simakov - Computational Modeling and Simulations | compmodel.org Reviews

https://compmodel.org

Computational Modeling and Simulations. This site is under construction. Center for Computational Research. University at Buffalo, SUNY. 701 Ellicott St., Buffalo, New York 14203. E-mail: nikolays@ccr.buffalo.edu. Below are several computational projects that I have been involved in. Is a toolkit developed by me to aid the molecular mechanical (MM) force field (FF) development for small drug-like molecule within the CHARMM/CGenFF Protocol. The work is done in Dr. Troy Wymore’s group. Olver) is GPU and CP...

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compmodel.org compmodel.org
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Nikolay Simakov - Computational Modeling and Simulations

http://www.compmodel.org/gaps.html

Computational Modeling and Simulations. Benchmark of CPU and GPU solver for calculation of single ion potential in α-hemolysin; next to columns is shown the improvement of GPU solver over CPU version run on 4 cores; the calculations were done with grid scale of 4 grid/Å and with grid size of 5143. Calculations were done on a single CPU desktop with Intel Core i7 930 processor and NVIDIA GTX 480 GPU. And the draft of our article here.

2

Nikolay Simakov - Computational Modeling and Simulations

http://www.compmodel.org/anton.html

Computational Modeling and Simulations. Anton MD Specialized Supercomputer. Below is a small video demonstrating the Anton capabilities. I use it during workshops to cheer up participants after long morning of instructions on Anton operations.

3

Nikolay Simakov - Computational Modeling and Simulations

http://www.compmodel.org/resume.html

Computational Modeling and Simulations. Address: 701 Ellicott St., Buffalo, NY 14203, USA. Professional web-site: http:/ www.compmodel.org. PhD in Chemistry, 2010. Carnegie Mellon University, Pittsburgh, PA, USA. Advisor: Prof. Maria Kurnikova. Thesis: “Theoretical Modeling of Current-Voltage Characteristics of Biological Ion Channels”. MS in Applied Physics and Mathematics, 2004. Moscow Institute of Physics and Technology, Department of Molecular and Biological Physics, Moscow, Russia. Project. XDMo...

4

Nikolay Simakov - Computational Modeling and Simulations

http://www.compmodel.org/pdynamo.html

Computational Modeling and Simulations. PDynamo: hybrid quantum chemical (QC) / molecular mechanical simulations.

5

Nikolay Simakov - Computational Modeling and Simulations

http://www.compmodel.org/index.html

Computational Modeling and Simulations. This site is under construction. Center for Computational Research. University at Buffalo, SUNY. 701 Ellicott St., Buffalo, New York 14203. E-mail: nikolays@ccr.buffalo.edu. Below are several computational projects that I have been involved in. Is a toolkit developed by me to aid the molecular mechanical (MM) force field (FF) development for small drug-like molecule within the CHARMM/CGenFF Protocol. The work is done in Dr. Troy Wymore’s group. Olver) is GPU and CP...

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Computational Modeling and Simulations. This site is under construction. Center for Computational Research. University at Buffalo, SUNY. 701 Ellicott St., Buffalo, New York 14203. E-mail: nikolays@ccr.buffalo.edu. Below are several computational projects that I have been involved in. Is a toolkit developed by me to aid the molecular mechanical (MM) force field (FF) development for small drug-like molecule within the CHARMM/CGenFF Protocol. The work is done in Dr. Troy Wymore’s group. Olver) is GPU and CP...

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