question about wrap atoms to its original coordinates

From: jnsong (
Date: Wed May 18 2011 - 00:06:20 CDT

Dear all,

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
3663 North Zhongshan Road
Shanghai, P. R. China

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