AW: question about wrap atoms to its original coordinates

From: Norman Geist (
Date: Wed May 18 2011 - 00:34:33 CDT


just load your system in vmd with a first frame where everything is there where it have to be, this is needed for reference, for example the crd or pdb file. Then load your trajectory and type the following to vmd console:

pbc unwrap -first 0 -last last

Frame 0 is needed for reference and must contain the original, unwrapped system.

If this doesn't work, try with additional "-sel protein"
If it is protein, if not, use another selection that fits your needs.
This is what works for me most of the time, if it doesn't for you. Get into the "pbc unwrap" command.

Best regards

Norman Geist.

-----Urspr√ľngliche Nachricht-----
Von: [] Im Auftrag von jnsong
Gesendet: Mittwoch, 18. Mai 2011 07:06
Betreff: namd-l: question about wrap atoms to its original coordinates

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

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:16 CST