From: Scooter Willis (HWillis_at_scripps.edu)
Date: Mon Feb 01 2010 - 13:35:37 CST
I am using VMD to move a long loop/turn and so far everything is working fairly well. In the startup process of NAMD it will on occasion exit with error from an atom going too fast. If I restart NAMD and reconnect it appears it will keep going. In the process a new frame is created in VMD. Once I get past 200 frames and occasional load balancing error(NAMD is running on a quad core processor windows XP with the +P4 parameter) I have been able to run the simulation through 10,000 timesteps.
It may be obvious but I can't seem to find docs or details on how to record or grab snapshots of the simulation via VMD. I would like to export PDB's of the various steps or make a movie from the IMD.
The project I am working on has two goals the first is to see if it is possible for a loop to come in contact with a fairly distant helix and based on VMD/IMD it is possible with minimum structural changes. Not sure how valid it is but was easy to do in VMD. I am also trying to get familiar with VMD and NAMD to see if we can use to the software explore structural changes in nuclear receptors based on various ligands and/or bound to DNA using HDX. If I start with a PDB (3DZY) structure bound to DNA I would delete the DNA and run in NAMD. When the proteins are not bound to DNA we know what regions of the DNA binding domain become dynamic or have high entropy. Any thoughts on experimental validation of NAMD simulations using HDX? I work in bioinformatics so trying to understand what is possible before presenting to the lab.
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