VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jan 06 2011 - 08:27:52 CST

On Thu, Jan 6, 2011 at 2:06 AM, Jervis Chu <nxchu_at_foxmail.com> wrote:
> Dear Kohlmeyer,
>
> Thanks for your kind reply. All done well for water molecules, but nothing
> happened on the XYZ file I mentioned. This really puzzled me.

a-ha. well, the first column of your .xyz file has the label
1 which VMD (or rather the molfile plugin for .xyz files)
will interpret as hydrogens, which are treated special.

in general using the .xyz file format is a bad thing, since
it contains so little information about your system.

you can, however, add information back by using VMD scripting.
e.g. if you want to turn those atoms to carbon atoms:

set mol [molinfo top]
set sel [atomselect $mol all]
$sel set name C
$sel set element C
$sel set mass 12.01
mol reanalyze $mol
$sel delete
unset sel
unset mol

axel.

>
> The parameters of the representation are:
>
> Coloring method: Name
> Material: Glossy
> Drawing Method: Dynamic Bonds
> Distance Cutoff: 1.6
> Bond Radius: 2.0
> Bond Resolution: 6
> Apply Changes Automatically: ON
>
> Regards,
>
> ________________________________
> Jervis Chu
> 2011-01-06
> ________________________________
> Re: vmd-l: How to show dynamic bonds?
>
> On Tue, Jan 4, 2011 at 2:58 AM, Jervis Chu <nxchu_at_foxmail.com> wrote:
>> Hi,
>>
>>  I generated an XYZ file, like
>>
>> 3
>> atoms
>> 1 0.0  0.0  0.0
>> 1 1.6  0.0  0.0
>> 1 2.9  0.0  0.0
>> 3
>> atoms
>> 1 0.0  0.0  0.0
>> 1 1.7  0.0  0.0
>> 1 3.0  0.0  0.0
>> ...
>> ...
>>
>> All atoms are carbon.
>>
>> I want to show dynamic bonds in VMD with cutoff distance 1.6. Can anyone
>> tell me how to do this on XYZ files.
> sorry for stating the obvious, but have you tried using
> the "Dynamic Bonds" representation???
> axel.
>>
>> Thanks in advance.
>>
>> Regards,
>> ________________________________
>> Jervis Chu
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA. 

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