Re: AW: question about wrap atoms to its original coordinates

From: jnsong (
Date: Thu May 19 2011 - 21:31:54 CDT

Dear Norman Geist,

Thank you very much for help!

I'm so sorry for the late reply!

I have two question to ask for your help.

In your MD simulation with NAMD, have you ever used "wrapAll on" and
"wrapWater on " in your NAMD input file?

You have mentioned "Frame 0 is needed for reference and must contain the
original, unwrapped system." in your last letter.
I can't grasp the meaning of "the original, unwrapped system".
You know, I have used "wrapAll on" and "wrapWater on" in my simulation.
So, as long as I run MD simulation of my system, the first frame must be
wrapped by NAMD itself.
Do you mean that I should not use ""wrapAll on" and "wrapWater on" in
NAMD simulation?

I have tried "pbc unwrap -sel "resname RBF""(RBF is the name of my
ligand) and now the ligand and the protein are in the same image, but
the case is not true for the water.
It seems that the water have some wrong bonds after I typed "pbc unwrap
-sel "water"", because it looks awful in VMD OpenGL for water.

Hope your reply and help!

Thank your very much!


On Wed, 2011-05-18 at 07:34 +0200, Norman Geist wrote:
> Hi,
> 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
> An:
> 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

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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