VMD-L Mailing List

From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Wed May 09 2007 - 11:27:29 CDT

Hi,

Thanks Olaf and Axel for your responses. I think I have resolved everything
now. pbcunwrap worked for me, then I used pbcwrap to wrap them back the way
I wanted it. I was having trouble because I didn't realize some of
the scripts had changed and were included in the plugin directory. The new
version of VMD is required to read DL_POLY V 3 formatted HISTORY files. I
don't know why the DL_POLY people just can't agree on a single format.

I think I am going to rewrite the trajectory program in DLPOLY to output
everything in dcd format anyway. These HISTORY files are quite a nuisance.
They have way too much information in them.

What's the difference between pbcjoin (which looks blank in the plugin
directory) and pbcunwrap?

Josh

On 5/9/07, Olaf Lenz <olenz_at_fias.uni-frankfurt.de> wrote:
>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi!
>
> Joshua D. Moore wrote:
> > I have been using DL_POLY version 3 to create trajectories. When I
> > visualize, it appears that all of the coordinates are wrapped with the
> > periodic boundary conditions. So the coordinates of some atoms are not
> > kept
> > with the molecule (as pbcwrap does with NAMD dcd files). So when bonds
> are
> > drawn they are somtimes extended across the box! Is there a way to
> unwrap
> > these coordinates? I tried using pbcunwrap from below, but I didn't
> have
> > much luck.
>
> - From your description, it's not easy to understand your problem. You'll
> find documentation on the pbctools in:
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
>
> The problems should not depend on the file format you're using, but on
> the simulation type. If I'm not mistaken, DL_POLY does standard MD
> simulations, so the pbctools should be able to cope with it.
>
> If I understand it right, DL_POLY writes the trajectiory such, that the
> coordinates are already wrapped into the central image. In that case,
> you will probably want to unwrap the coordinates, to make the
> coordinates continuous over the different frames of the trajectory,
> avoiding the jumps caused by the wrapping. To do that, you can use the
> function "pbc unwrap". If that doesn't solve your problem, then please
> try to specify your problem more precisely.
>
> Best regards
> Olaf
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.1 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFGQdI3tQ3riQ3oo/oRArFAAJ0eaP75A7gptsVkDO7KuQHimYt8PwCfSNz7
> 2S36RGGDAvdC/aKlPYDLlSg=
> =DTMp
> -----END PGP SIGNATURE-----
> 

-- 
------------------------------------------------
Joshua D. Moore
Graduate Student
North Carolina State University
Dept. of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC  27695-7905
Phone: (919) 513-2051
Fax:   (919) 513-2470
Email:  jdmoore_at_unity.ncsu.edu
------------------------------------------------