However, even moderately effective docking is computationally expensive. In other words, conclusions like “The RMSD went up” do not tell us why people get cancer or what to do about it.Įveryone does simulations different ways and for different specific reasons, but I’d argue that the most directly valuable question that people can try to answer is “how does this simulation help me make a drug?” The normal way for people to use a protein structure to make a drug is by using “docking” software, which tells them how likely a given small molecule is to fit into a binding site. There are a growing number of tools that try to quantitatively answer the question of “what in the world just happened in this simulation”, but they often do abstract analyses with no clear actionable output. However, what usually happens is that scientists run simulations (at great computational cost), and then see a big protein wiggling around, and have no idea what to do with it. Molecular Dynamics simulations are getting really popular in our field of science. Gcq#395: “It was something to at least have a choice of nightmares” (Joseph Conrad) Please don’t hesitate to complain - The problems that give you the hardest time are the ones I’ll focus on fixing first! You can expect far less stability and user-friendliness from this software than you could from things like VMD. ![]() I also have two other essentially full-time projects. This is controlled with the correct tension on the rotor with the PPM and powder hopper against the disk with the Auto Disk.Jeff’s note: I am the current lead developer of POVME. It will etch the heck out of the nylon and it will never work right. The worst thing that can happen to this unit and the Auto Disks is to have powder get caught between the rotor/wiper and the rotor/disk. Oh, that unit above was purchased in 1999 and has dropped over 150,000 charges! I guess the little bit of sprinkling is expected but I durn sure am not going to replace my old friend! Will update with photos of the work later today, need to get back on my tractor as coffee time is up. The new unit had zero grains of powder on the white paper. Anyway, I spent just a minute for a couple rotations of lapping, cleaned it, set it up, and did the same test as above. I just did another, I bought a couple additional units for my Load Masters as I'm moving some rifle loading to them. The 500 has been discontinued so I would suggest 600. I use Cloverleaf 500 grit silicon based lapping compound. I have a lot of powders on my shelves and it is the only way I can keep up with it. On the VMD tab you can add rows for non listed powders or for calculating powders using different delivery systems Auto-Disk, Dipper, PPM, etc. I even made a VMD Calculator, in xls format which is on my server as a download (click the highlighted link). Like I noted I'm a Lee guy and load a lot, about 12K rounds a year, and the VMD thing against a cc calibrated measure is indispensable. So, with each new container of powder, I establish the lot's VMD and mark the container with the number with a Sharpie. The published VMDs are standard but there is quite a bit of variations against the standard. These to marks stay aligned so that the metering rod works against VMD calculations. One thing that I also do to the PPM is adjust the metering rod, thimble, and metering chamber to establish a "zero" and then mark both the thimble and metering chamber barrel. I reload quite a bit and just don't have problems with mine after prepping them. I use a lot of powders like BL-C(2) and H355, so I adjusted the Rotor Tension Adjustment Screw to my satisfaction with those powders. ![]() I used 600 grit and then cleaned it up with Dawn detergent. ![]() What I did is assembled them with lapping compound between the body and rotor, and then turn them a bit. I use a Lee Perfect Powder Measure, actually have five of them on different presses.
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