VMD-L Mailing List

From: Lan He (Lan.He_at_asu.edu)
Date: Thu Oct 08 2009 - 13:29:10 CDT

Hi, Axel and Olaf,
 
I'm sorry I still have to ask these simple questions about displaying box in VMD. I confirmed I have installed the latest version 1.8.7 and pbctools included in it. I read the documentation and tried to carry out the examples. Unfortunately, when I just run the pbc set cell command like the example " pbc set 10.0 10.0 10.0 -all", the errors occured. The error is like"ERROR: pbcset: unknown option: 10.0". Is this because of the command with the unknown format? I just want to set the cell and draw the celll. Why can't I use the commands "pbc set " and " pbc box"? Could you help me fix it? Thank you so much!
 
Lan

________________________________

From: Olaf Lenz [mailto:lenzo_at_mpip-mainz.mpg.de]
Sent: Thu 10/8/2009 0:03
To: Axel Kohlmeyer
Cc: Lan He; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: how to display the periodic box in VMD

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi!

Axel Kohlmeyer wrote:
> On Wed, 2009-10-07 at 15:51 -0700, Lan He wrote:
>> I get the problem with displaying the periodic box in VMD. I downloaded pbctools.tcl and ran the codes of pbctools.tcl in VMD TkConsole. Then I thought I can used the commands in pbctools. But, sort of, not like this. I tried to use draw_pbc_vectors and I failed. I'm not familar with tcl code. So, I don't clearly know about the arguments in each command of pbctools. I know, it is easy to draw the defined box in OPGL. using lines to connect the defined points of the specific box can generate the box image (i.e. rectangular box or cubic box). I think the tcl codes in pbctools should have described how to draw. Unfortunately, I don't know how to use these commands. I guess I must miss something. Could anyone give me some suggestions? Thanks a lot!
>
> pbctools.tcl is _long_ obsolete.

As Axel didn't mention where: The documentation of the pbctools plugin
that is included in VMD 1.8.6 and 1.8.7 can be found here:

        http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

If I assume that you have one of these versions, it should be enough to
type "pbc box" in your Tk console to generate the box you want.

Best regards
        Olaf

- --
A: Because it messes up the order in which people normally read text.
Q: Why is top-posting such a bad thing?
A: Top-posting.
Q: What is the most annoying thing in e-mail?
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v2.0.4-svn0 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFKzY7atQ3riQ3oo/oRAjbPAKCQwJRJcVbpygWMlSeKqhwSo2nW0ACffp7O
RLMmL9YdKBPfrJXEKWFkHbQ=
=cbGP
-----END PGP SIGNATURE-----