Re: query about wrapped coordinates: Problem SOLVED

Date: Wed May 09 2007 - 09:22:29 CDT

Hi all,
    The problem of unwrapping coordinates of any segment of the system that has been wrapped during periodic runs can be solved in this way. There has been a long mail-exchange on mailing list, so i thought of sharing the steps it took me to do that for future use:

1. Load .DCD and.PSF files of your simulation run.
2. IN case you had "DCDunitcell yes" in the config file, then you can skip this step. If not, no worries the way is here:

   [a] find .xst files of your run and find values of a,b,c (unitcelldimensions).
   [b]. Go to tcl/tk interface in the loaded trajectory, then run these commands or save in a script named unitcell.tcl and run it
 # Find the number of frames
set nframes [molinfo top get numframes]

# Loop over all frames in the dcd files
for {set i 0} {$i < $nframes} {incr i} {
  molinfo top set frame $i
  molinfo top set a xx (where xx is value of 'a' from .xst file)
  molinfo top set b yy
  molinfo top set c zz

3. Then, source the "unwrap.tcl" scipt provided in previous threads by Gianluca

4. after sourcing the script, type:

  unwrap "seltext" ---the seltext can be -all/protein/protein and segname X/ or anyother correct vmd selection you like to unwrap.

I hope this should help people.

Harish Vashisth (Ph.D Candidate)
CAT-361,Chemical & Biological Engg.
Drexel University, Philadelphia, PA
office: 215-895-5823

----- Original Message -----
From: Cesar Luis Avila <>
Date: Tuesday, May 8, 2007 9:46 am
Subject: Re: namd-l: query about wrapped coordinates

> If you look once again at molinfo documentation you will notice
> that you
> only set a b c for the current frame. For a trajectory you should
> use a
> loop as suggested by gianluca.
> escribió:
> > Hi Dr. Gianluca and Cesar,
> > Thanks for this information. I took value of a,b,c from the
> .xst file of my run and loaded the trajectory as usual, then used
> the molinfo commands for setting a,b,c values. Sourcing the script
> and applying command unwrap protein again gives the error:
> > " Box abnormally small or no box size info available"
> > For a moment i see the protein inside the box but when i slide
> the frames, the situation is same, i can see it going in/out.
> Please suggest what might be wrong with the way I am doing.
> > Thanks again.
> >
> > Harish
> >
> >
> > -

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