Diary of the 2003 Summer School on Theoretical and Computational Biophysics

Friday, June 6 -- David Zhang

David Zhang It has been a very fruitful week so far, and today's lecture was the last of the week. Prof. Todd Martinez gave lectures on QM/MM methods. Not surprisingly, many participants were not very interested in the lectures. I wasn't expecting much anyway. To be fair, I think Prof. Martinez did a good job in summarizing the different methods in QM. He was humorous and I laughed loud when he said "Chemists are the Fourier transform of Physicists."

I was again amazed by the devotion of the summer school organizers. Professor Klaus Schulten has been sitting on almost all the lectures. He didn't hesitate to stop the lecture to let us ask questions. When the first lecture ran late, he suggested us to have an early coffee break. Many of his group members were also present in the lecture room.
"I was again amazed by the devotion of the summer school organizers. Professor Schulten... didn't hesitate to stop the lecture to let us ask questions."

The weather wasn't very good. It was actually pretty clear in the morning when I left Hendrick House. But it started raining half way through the lectures, and was still raining heavily at lunch time. My plan was to go to the Thai restaurant to taste their beef shrimp noodle. Unfortunately I did not bring my umbrella (I later brought my umbrella in many days that wasn't raining). I waited in hope the rain would stop, but ended up skipping my lunch.

The rain did not stop when it was time for the afternoon hands-on session. We had to run over to the lab in the rain. The materials for the afternoon session wasn't about QM/MM at all. It would be nice if we could do some real QM/MM stuff. I guess it isn't trivial to prepare materials for such a practice, especially QM/MM itself is not a matured method. Still, I find the tutorial quite helpful. I have always used Antechamber in Amber to set up new systems. It is nice to learn how to do it in Charmm format. The tutorial provided most of the components of the topology file, and we only needed to fill out some missing parameters.

Dinner time I went to visit an old friend of mine here. He is an assistant professor, and he started his group three years ago. We had a long chat about almost everything from research to life. He gave me a tour of his lab. It seemed that he has already has a well established lab with lots of space.

By the end of the tour I found I was late for the evening session. My stomach complained strongly when I tried to head back to the computer lab. Instead, I headed to the Thai restaurant to taste the shrimp noodle. By the time I was back to the lab, I was 40 minutes late. All the doors to the Engineering Lab and Everitt Lab were locked, and I couldn't get in. I had to wait outside and finally I saw someone passing by. Out of desperation I asked if he had access to the building. Thank God, he let me in.

At the evening session I spent some time on finishing the tutorials. I then chatted with others in BioCoRE. Tomorrow some of us are going to Chicago, and we were very excited about it. The lab attendants were very helpful and let us stay for an extra half hour. Thanks, guys.

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