VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Feb 22 2011 - 07:19:28 CST

On Mon, Feb 21, 2011 at 11:09 PM, mjyang <mjyang_at_hku.hk> wrote:
> Dear VMD users,
>
>    I am going to unwrap a trajectory file produced by NAMD. Since the dcd
> file is very large, it takes a lot of time to do this by vmd graphical mode.

> I think it will be faster when using the python script model.

no, it won't. the script does the exact same think and graphics
are not involved in running pbc unwrap.

> I read the vmd mannual and found some related commands.
>
> The script I wrote is as follows:
> ---------------------------
> load ('psf', 'system-solv-neutral.psf', 'dcd', 'system3.dcd')
> pbc -unwrap -first now
> write dcd test.dcd skip 10 sel all
> -----------------------------

you didn't read well enough.
this script doesn't make any sense at all.
furthermore, the pbc command is part of
a Tcl plugin, so you cannot call it directly,
but hand it to the Tcl interpreter. overall,
you would be better off using Tcl scripting.
there are sufficient examples for that in the
user's guide and there are VMD scripting tutorials
as well as Tcl scripting tutorials available on
the web.

> But it halted with errors each time.

no surprise. GIGO.

> So I request your kindly help.

you first have to help yourself to some more
understanding of what you are doing. ;)

cheers,
    axel.

> Many thanks.
>
> Mingjun
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.