Application tools

From HP-SEE Wiki

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

Gaussian series of electronic structure programs are used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Starting from the fundamental laws of quantum mechanics, Gaussian predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments. General description of Gaussian features are available at Gaussian official web site (www.gaussian.com) and HP-SEE Wiki [edit] Software Stack and Technology Watch / Libraries section (http://hpseewiki.ipb.ac.rs/index.php/GAUSSIAN).

Gaussian03 is ported to PARADOX 32-bit cluster at the Institute of Physics Belgrade using Linda 7.1 (Gaussian native unit for the parallel processing). Typical usage in CompChem http://wiki.hp-see.eu/index.php/CompChem application id the following:

• Mechanisms of the chemical reactions were examined. In the reaction of the cylohexanone with the bromoform, two alternative mechanistic pathways were examined. Submitted.
• Full geometry optimizations on the high level of theoaty, typical DFT or MP2, or the single-point calculations on the geometries obtained on the semi-empirical level of theory, for the diverse set of compounds were performed, aimed to extract molecular descriptors suitable for the linear-free energy relationships (applied in part in Tetrahedron Letters 53 (2012) 553), or for the three-dimensional quantitative structure-activity relationships.

Efficient scaling at PARADOX cluster was obtained using 4 nodes.