Re: query about wrapped coordinates: Problem SOLVED

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed May 09 2007 - 12:28:27 CDT

Wouldn't it be a good idea to have DCDunitcell on per default in the NAMD
code?

A small correction: the unwrap script was written by somebody else
(Jerome). I only forwarded it. (Just to get the credits right :))

The unwrap script can be found here:

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/att-4720/DOC_unwrap.html

Gianluca

On Wed, 9 May 2007, hl332_at_drexel.edu wrote:

> 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
> -------------------------------------------------
> Harish Vashisth (Ph.D Candidate)
> CAT-361,Chemical & Biological Engg.
> Drexel University, Philadelphia, PA
> office: 215-895-5823
>
> ----- Original Message -----
> From: Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar>
> 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.
> >
> > hl332_at_drexel.edu 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
> > >
> > >
> > > -
>
>
>

-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
                    +1 (206) 685 4435
                    +1 (206) 714 4303
                    http://biocroma.unizh.ch/gianluca/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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