Application tools

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AMBER

Section contributed by IICT-BAS

After testing the performance of modules SANDER and PMEMD of AMBER v.11 with respect to the number of processors and nodes requested, using as a test case cyclodextrin with 100 glucose units (CD100; 2100 CD-atoms and 37459 water molecules; 2.0 ns molecular dynamics simulation; total steps 1000000), it is proceeded further by executing molecular dynamics conformational search with duration 60.0 ns. It is found as an optimum to use module PMEMD with 64 processors (8 nodes with 8 (of 16) processors per node).

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