Application tools

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Revision as of 17:34, 16 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). It is basically well known that the PMEMD module should be used when the use case allows for it, since it is more scalable. In principle using more CPUs is beneficial with respect to the total running time, but the efficiency drops,

GAUSSIAN

Section contributed by IPB-FCUB

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

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

• Study of mechanisms of chemical reactions: in the reaction of the cylohexanone with the bromoform, two alternative mechanistic pathways are examined.
• 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.

NAMD

Section contributed by IPB-FCUB

NAMD is a parallel classical molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit Ethernet. General description of NAMD features are available at NAMD official web page (http://www.ks.uiuc.edu/Research/namd/) and at HP-SEE Wiki Software Stack and Technology Watch / Library (http://hpseewiki.ipb.ac.rs/index.php/Libraries) section.

Currently, NAMD-2.6 and NAMD-2.8 (including betas) versions are ported on PARADOX cluster. Both versions are compiled under Charmrun. CompChem (http://wiki.hp-see.eu/index.php/CompChem) application uses NAMD for Molecular dynamics simulation of:

• Set of small biologically active molecules in isotropic or anisotropic explicit solvents, typically during 20-30 ns. Biasing forced (adaptive biasing force) was used in majority of simulations to obtain free-energy landscapes. Analysis of results connects dynamical behavior of molecules with their selectivity (tumor vs. healthy cells). Two relatively novel concepts, as described in Drug Discov. Today 13 (2008) 285, and J. Chem. Theory Comput. 6 (2010) 35, were merged.
• Simulations similar as described above were performed, using implicit solvent model, aimed to obtain conformations of flexible molecules suitable for linear-free energy relationships. Unique concept so far, Tetrahedron Letters 53 (2012) 553.
• Dynamical behavior of novel fruit allergen isolated in our laboratories, uninhibited, or inhibited were examined. Typically during 5-10 ns, using counterions and explicit solvation with large solvent cluster to simulate experimental conditions (mainly ionic strength). Different ionization states of protein, under different pH values as applied in experiments, is also considered. Those simulations aim to explain experimental observations: different electrophoretic mobility of inhibited and uninhibited protein, as well as difference of proteolytic digestion between the inhibited and the uninhibited protein. Article in preparation.
• Long, typically 60-80 ns, unbiased simulations of ‘approach and entrance’ of acetylcholine esterase dual, non-covalent inhibitors, to enzyme active site. Explicit solvation by large solvent cluster was considered in the each simulation. Set of 10 compounds was simulated so far. Aim of the study is to improve potency of compounds. Such compounds should cure symptoms of the Alzheimer disease. So far one communication submitted.
• Steered molecular dynamics, or unbiased molecular dynamics simulation (typically 10 ns) for the design of the peptidomimetics that should act as inhibitors of the protein-protein interactions. Such compounds should exert activity toward targets involved in life-threatening diseases. Article in preparation.
• Minimization and the equilibration of the few large solvent clusters of the different composition, aimed to be used in standard simulations.

Scalability of NAMD 2.8 on PARADOX cluster performed using native NAMD benchmark (http://www.ks.uiuc.edu/research/namd/, 10000 steps, 92,224 atoms, 12 Å cutoff + PME every 4 steps, periodic boundary conditions) is given at figures below.