Category Archives: Modeling & Simulation

Hundred nanoseconds a day

By Deepak Singh | Published: June 14, 2009
Image by vitroids via Flickr 100 nanoseconds a day. 100 nanoseconds a day. 100 nanoseconds a day That is amazing. I used to get supercomputing time to do 100 ns simulations during my PhD and those used to last days, but that’s exactly what NAMD has achieved recently. A recent review article by [...]
Also posted in Computing, Life Science | Tagged , , | 2 Comments

Modeling molecular systems

By Deepak Singh | Published: April 21, 2009
Eric Drexler is one of the smarter people I know. We don’t always agree. In fact, we disagree a lot, but he is always an interesting read. In a recent post on the Macromolecular Modeling Blog (cross-posted to his blog) Eric writes about macromolecular modeling in the context of one of his [...]
Posted in Modeling & Simulation | 2 Comments

Frameworks for modeling and simulation

By Deepak Singh | Published: March 27, 2009
Recently, I have found myself putting my product manager hat back on and trying to imagine how I might design the next-gen molecular simulation system. Since these thoughts tend to be scattered over the few minutes I am not working, they are anything but well formed. In my mind, such a system would not be just [...]
Also posted in Software & Internet | Leave a comment

Thirty years of biomolecular simulation

By Deepak Singh | Published: March 22, 2009
Image via Wikipedia Adam Kraut blogs about Wilfred Van Gunsteren’s talk on 30 years of (bio)molecular simulation. This is a topic very dear to my heart since that’s kinda what I am supposed to be good at (or at least was) and it’s also one where I feel that we haven’t been as innovative as [...]
Also posted in Physical Science | 1 Comment

Paying attention to simulation

By Deepak Singh | Published: January 31, 2009
Thinking a lot about the role of computing and informatics in modern science. As I like reminding people, that while many put me in the “bioinformatics” category, my training is in molecular simulation. Which is why a post by Joe Landman on dynamical systems and climatology caught my eye, particularly the following quote HPC [...]
Also posted in Computing | Leave a comment

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