Pittsburgh Supercomputing Center

The work was supported by NIH grants P01 DA-12923, P20 HL69733, and K05 DA-00060 (to HW). MF is supported by NRSA T32 DA07135. Computational support was provided by the National Science Foundation Terascale Computing System at the Pittsburgh Supercomputing Center and by the computer facilities of the Institute for Computational Biomedicine of the Mount Sinai School of Medicine. 

This work was supported by NSF Grants No. DMR-9500858 and DMR-9100063 and ONR Grant No. N00014-91-J-1516. The calculations were carried out at the Pittsburgh Supercomputing Center. 

Stocks, Wang, and their colleagues used an extremely powerful computer made by Cray, Inc., called an XT3, to simulate the behavior of a few thousand atoms in the material. This computer, located at the Pittsburgh Supercomputer Center, has 2,048 computer processors to speed up operations it so fast it is called a supercomputer. Even so, a simulation of 14,400 atoms, including all their important interactions, required 50 hours of computer time. (Since the computer was shared with other users, not all the processors were devoted to this simulation.)... 

This material is based upon work supported by the U.S. National Science Foundation (grant CBT-8708734). Supercomputer time was provided by the Pittsburgh Supercomputing Center. Additional computational recourses were provided by the Cornell Theory Center. 

We would like to thank the NIH (GM-29072) for their generous support of this research. The Pittsburgh Supercomputer Center and The Cornell Theory Center through a MetaCenter grant are acknowledged for generous allocations of computer time. 

This work was supported by the National Science Foundation Grant Nos. DMR-84-16046 (H. Krakauer) and DMR-84-20308 (P. B. Allen), and by the Office of Naval Research. Computations were carried out under the auspices of the National Science Foundation at the Cornell National Supercomputer Facility and at the Pittsburgh Supercomputer Center, as well as on the Naval Research Laboratory Cray X-MP. 

This work is supported by NSF Grant PHY-9002863. Some of the calculations reported in this work were performed at the Pittsburgh Supercomputing Center. The author would also like to acknowledge the fruitful collaboration with Klaas Allaart, Mario Brand, Arturo Polls, Angels Ramos, Gust Rijsdijk, and Brian Vonderfecht, which has produced the results that were discussed in this paper and the permission from the NIKHEF group to use Fig. 1. 

Financial support from the National Institutes of Health (GM51501-01) and computational support from the Pittsburgh Supercomputing Center and NCI s Frederick Biomedical Supercomputing Center are appreciated. 

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This work was supported in part by the National Science Foundation through NSF Grant No. CHE-1223988 and TeraGrid resources provided by Pittsburgh Supercomputing Center. 

As conformational sampling is the main bottleneck in the simulation process, efforts have been made to parallelize AMBER for use in both molecular dynamics and free energy calculations. A recent collaboration involving, in addition to AMBER authors, Mike Crowley of the Pittsburgh Supercomputer Center, has led to a very exciting parallel version of the program which enables each nanosecond simulation of a 40000 atom system, the thyroid hormone receptor, using PME electrostatics to be completed on 128 processor of the CRAY T3E in about half a week, about six times faster than the calculation would have taken on the previous version of the software, which was quite efficient on the CRAY T3D. 

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