From: Norman Geist (norman.geist_at_uni-greifswald.de)
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.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von jnsong
Gesendet: Mittwoch, 18. Mai 2011 07:06
Betreff: namd-l: question about wrap atoms to its original coordinates
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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