Dr Cool Santa wrote: > Currently in the lab we use Schrodinger and we are looking into NWchem. > We'd be interested in knowing about software that a chemist could use > that makes use of a parallel supercomputer. And better if it is linux. >
Clarification: I supported Schodinger up until a year ago. Unless things have changed, Jaguar is the only Schrodinger application that can truly make use of a "parallel" supercomputer. The other Schrodinger programs perform calculations that are embarassingly parallel and require no inter-process communications during calculations. In these cases, the data to be analyzed is broken up into smaller pieces that are analyzed individually by the computers with no communication between them. When they are done, the main program reassembles their output to a final result. This is parallel computing, but doesn't require a "parallel supercomputer". It works great, BTW. OpenEye provides some commercial computational chemistry software (conformer generation, docking, etc.), that uses parallel code. Their code uses PVM instead of MPI, which makes OpenEye kind of an odd duck. Last I spoke to OpenEye, they were planning on porting their code to MPI, but don't know if that's been done yet, since I no longer support their software. If you're doing molecular simulations, there's LAMMPS ( Large-scale Atomic/Molecular Massively Parallel Simulator), which is open-source. I actually submitted a *very* small patch to when I ported it to IRIX 6.5 a few years ago. NAMD is also parallel, but I don't know much about it. I compiled it, installed it, but then I don't think the comp chemists ever used it (don't you hate that?). -- Prentice _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf
