From: jnsong (jnsong_at_itcs.ecnu.edu.cn)
Date: Wed May 18 2011 - 00:06:20 CDT
I have used NAMD to perform MD simulation on a membrane protein system.
But in the trajectory, my membrane protein and its ligand are in
different images, this brings me difficulty to analyze the simulation
results. Take distance between an atom in ligand and another atom in
protein for example, the value of distance will be very large if protein
and its ligand are not in same image.
Would you please to tell me how to solve wrap problem in NAMD?
In my simulation, I have "wrapALL on" and "wrapWater on".
Thank you very much!
-- Jianing Song Ph. D. Student Institute of Theoretical and Computational Sciences Dept. Phys. East China Normal University 200062 3663 North Zhongshan Road Shanghai, P. R. China
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