[DIYbio] Re: Molecular Dynamics

Do you receive a huge speed-up from CUDA? 

I was doing some basic MD. I wanted to compare simulations of proteins that start from X-ray structures or NMR structures. One would predict that because of the nature of crystals that some X-ray structures might simulated differently due to starting in unnatural conformation. However, people think that X-ray crystallography is the gold standard in structural biology, predicting structure &c. when some of these structures are probably slightly, majorly off. I need to redo it though actually using NMR and X-ray structures from the same proteins instead of different proteins.

I was running on a Quad core but it might be good to just invest in something I can run CUDA with.

On a small protein <100 amino acids in a water box I could run maybe 1.5 nanoseconds a day.

On Wednesday, October 31, 2012 2:55:20 AM UTC-5, rwst wrote:

I have tested NAMD with my NVIDIA and CUDA, very impressive. Now I would like to do protein folding with that setup,
applying forces from coupling analysis and a simulated annealing protocol. That's the idea, anyway. Did you know that
decades of research on human hemoglobine turned out to be wrong and you can do it right by patient application of MD?
There are so many interesting things to visualize, receptor docking, enzyme allosterisms, somebody stop me...

On Wednesday, October 31, 2012 3:53:26 AM UTC+1, Josiah Zayner wrote:

Is anyone working on MD simulation stuff?