Category Archives: multicore
Overview NAMD simulates molecular motion, especially of large molecules so it’s often used to simulate molecular docking problems. One particularly interesting class of docking problem is the interaction of protein molecules with other molecules such as the cell membrane. The … Continue reading
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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 open science grid is a distributed heterogeneous network of computing clusters. Its infrastructure and protocols allow members to submit high throughput compute jobs for remote execution. All use is authenticated and authorized via a PKI infrastructure which associates jobs … Continue reading
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