Author Archives: admin

9:30 am – 5:00 pm, 9:00 pm – 12:15 am PH project replotting all histograms — no more collecting all the big stuff into the last bin, this was confusing. made new figure-producing figs (actually just histograms, the images are … Continue reading →

10:00 am – 12:45 am More simulation troubleshooting Experimenting with weaker attractive forces energy = (“index*epsilon * .000000001 * (step(r-rm)*(r-rm)^4 * (1- step(r-2*rm))+ (rm)^4*step(r-2*rm));” “index=index1*index2″) reasonable scaling 10 fold stronger bonding: “sticky8” simulation energy = (“index*epsilon * .00000001 * (step(r-rm)*(r-rm)^4 … Continue reading →

10:00 am – 5:00 pm, 10:00 pm – 12:30 am Lab stuff Finally found and installed drivers for Cajal’s AMD Radeon 6900 graphics card (this card is still driving the monitors). installed new NVIDIA Quadro K4000 for GPU computing (still … Continue reading →

10:20 am – 11:15 pm New simulations sticky polymer simulations. same as blue simulations but reduce binding energy 10 fold. index*epsilon * .0001 * (step(r-rm)*(r-rm)^4 * (1- step(r-2*rm))+ (rm)^4*step(r-2*rm)); now running with 10 polymers, log scaled from 10 to 500 … Continue reading →

9:30 am – 5:45 pm Simulations To Analyze OpenMM free Polymer sims Odyssey Matlab periodic bonds OpenMM free Polymers Only a single run, but not quite the right scaling — expect 0.60. And a y-intercept at 0. See previous simulations … Continue reading →