Application tools
From HP-SEE Wiki
(Difference between revisions)
(Created page with "=== 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 req...") |
|||
| Line 4: | Line 4: | ||
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). | 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). | ||
| + | |||
| + | === GAUSSIAN === | ||
| + | |||
| + | ''Section contributed by IPB-FCUB'' | ||
Revision as of 19:12, 14 April 2012
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).
GAUSSIAN
Section contributed by IPB-FCUB
