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Protein Tutorial with PyMOL and GROMACS

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You may have been patiently waiting for the first installment of my nanotechnology blog and you're right to expect great things. I have found myself pushing more and more stuff onto my stack and there will be a time for popping all those off the stack. The first one is what I've been working on the past three weeks.

There are plenty of tutorials for GROMACS but because I had a bunch of problems using it, I thought I would write another one. My tutorial is based on this one, so if you want the original, look there.

First, we need a molecule to minimize*. We could use 1OEI, but let's start with a blank slate. Minimizing an already minimized protein is kinda boring.

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Plans for March 2014

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Dear friends,

I've told some of you about my big plans in March, but I wanted to write a big open letter to everyone for good measure. When I graduated college, I feel really silly for not sending an e-mail to everyone I knew telling them that I had graduated and was looking for a job. Now that I'm switching careers, I thought it'd be wise to send an e-mail. This time I'm not looking for a job.

I'm leaving the security industry in a few months to pursue independent research in nanotechnology. It's taken a long time for me to achieve my goal of feeling confident about my financial situation so that I can pursue research without spending years in academia as a grad student or as a researcher working on someone else's project in industry. It's not that I think those things are bad, in fact they can be great, just not a good fit for me. I've been very independent for pretty much all my life and I'm impatient waiting for nanotechnology which I predicted would be in full swing years ago. If you're not familiar with nanotechnology, there's a lot of very cool science going on which is headed toward the molecular scale, smaller even than Intel's new 14nm resolution CPUs. Applications are wide-ranging and could change the way we make things. Not just computers, not just medicine, and not just solar panels. It's the reason I got my Bachelor of Science in Physics and had I been smarter about it, I may have gotten a research job back then and be where I am right now but with 10 years of research behind me. So this is me righting myself.

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Talk to AI3

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by Javantea
Nov 19, 2013

I wanted to post this to my Mexico blog here since I just told people that I'd be blogging there instead of here for the next two weeks, but I decided that a travel blog shouldn't have such an important announcement.

AI3 now has an alpha natural language interface. It doesn't yet query the database like it should, but it will. For now you'll have to be satisfied with thousands of possible conversations. What is a brilliant technology without a tutorial? Here we go.

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