Category Archives: pmemd
Our first researcher using Amber PMEMD on the OSG reports molecular dynamics are four to eight times faster on the OSG than with the infrastructure she had access to previously. That’s for the all CPU version, i.e. without the Nvidia … Continue reading
Molecular Dynamics Proteins are important and their structure complex. And then they move. The way they move determines how organisms work … or fail. The shape of the protein determines its function so motion means its shape is in flux … Continue reading
PMEMD for OSG is live. Gratia statistics for January: All runs are 8-way parallel MPI jobs so we get eight hours of CPU time per hour of wall time.
The Goal RENCI’s working with researchers interested in running high throughput parallel molecular dynamics simulations on OSG. Amber9 PMEMD The program we’d like to execute is called PMEMD (Particle Mesh Ewald Molecular Dynamics). PMEMD is a high-performance, parallel component of … Continue reading
Baby steps. This is pmemd compiled against native MPI libraries executing on the RENCI Blueridge cluster. The job submission workflow uses the RENCI-CI script library. The job_run script uses Globus tools to transfer the pmemd application and input files to Blueridge. … Continue reading
Since my earlier post about building Amber9 I’ve learned that the Amber code base contains a new development stream and a highly parallel performance oriented development stream. The executables these create are called sander and pmemd respectively. The high performance … Continue reading