This report introduces hybrid implementation of the Gromacs application, and provides instructions on building and executing on PRACE prototype platforms with Grahpical Processing Units (GPU) and Many Intergrated Cores (MIC) accelerator technologies. GROMACS currently employs message-passing MPI parallelism, multi-threading using OpenMP and contains kernels for non-bonded interactions that are ...

One of application that needs high performance computing resources is molecular d ynamic. There is some software available that perform molecular dynamic, one of these is a well known GROMACS. Our previous experiment simulating molecular dynamics of Indonesian grown herbal compounds show sufficient speed up on 32 n odes Cluster computing environment. In order to obtain a reliable simulation, on...

Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials ...

Homology models of amidase-03 from Bacillus anthracis were constructed using Modeller (9v2). Modeller constructs protein models using an automated approach for comparative protein structure modeling by the satisfaction of spatial restraints. A template structure of Listeria monocytogenes bacteriophage PSA endolysin PlyPSA (PDB ID: 1XOV) was selected from protein databank (PDB) using BLASTp with...

The increasing gap between plentiful computing elements and limited memory bandwidth makes it increasingly difficult and sometimes even infeasible for HPC community to port more applications onto many-core processor archi‐ tectures. The Sunway many-core processor SW26010 used to build the Sunway TaihuLight System contains a total of 260 heterogeneous cores. All these cores can be divided into 4...

Heterogeneous administrative domains, operating systems (OS), and libraries make it difficult for computational scientists to fully utilize metacomputers and grids. Dealing with the presence or absence of features on, say, different clusters, adds complexity. How can a user or high-performance computing (HPC) application abstract out the heterogeneity? One possible solution is to use a virtual ...

MOTIVATION GSATools is a free software package to analyze conformational ensembles and to detect functional motions in proteins by means of a structural alphabet. The software integrates with the widely used GROMACS simulation package and can generate a range of graphical outputs. Three applications can be supported: (i) investigation of the conformational variability of local structures; (ii) ...

We investigate the parallel scaling of the GROMACS molecular dynamics code on Ethernet Beowulf clusters and what prerequisites are necessary for decent scaling even on such clusters with only limited bandwidth and high latency. GROMACS 3.3 scales well on supercomputers like the IBM p690 (Regatta) and on Linux clusters with a special interconnect like Myrinet or Infiniband. Because of the high s...