From: xyhu1127 (xyhu1127_at_gmail.com)
Date: Thu Jan 14 2010 - 19:17:18 CST
I wrote an e-main yesterday using 163.com but you can't read any text of it. So i use gmail instead.
I am a new user of NAMD.
My system contained a protein and a small ligand. The system was solvated in a water sphere. The radius of the sphere is 25A. When i tried to equilibrate the system after minimization, there was something wrong. The energy in the log file were as follow: "ENERGY: 2300 1.#QNB 1.#QNB 0.0000 0.0000 0.0000 0.0000 83951.4201 1.#QNB 1.#QNB". By checking the dcd file in the VMD, I found that the water were missing and only the protein and ligand left. I don't know whether it is because of the fixed atoms. Can anyone tell me why and how to solve this problem?
The configure file is attached to this mail.
There is another question. As the time step was 1 fs, if the rigidBonds was to "water", the error is "bad global exclusion count" when simulation. Should i increase the cutoff to avoid this problem or change the rigidBonds to "none"?
Thanks for your help.
Xiaoying HU, Ph.D candidate
Beijing University of Chemical Technology
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