VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Mar 31 2022 - 09:05:33 CDT

This information has no impact on what I already explained. 

--
Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!ppk9OrMrZTJP1ZC1iPNxJIehZCfAkBY2HvIhFTVyfdObdQ3mYwoviS2fUmeFmSXsdQ$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste, Italy
On Thu, Mar 31, 2022, 09:57 maxim todoru <mtodoru_at_gmail.com> wrote:
> The structure was stored in .xyz format.
>
>
> Le mer. 30 mars 2022 à 13:15, Axel Kohlmeyer <akohlmey_at_gmail.com> a
> écrit :
>
>> VMD uses the topology information provided in your input and if there is
>> no topology data, it will do a heuristic bond search based on a list of
>> covalent radii with the constraint that any atom whose name starts with H
>> is considered a hydrogen and then can have only one bond.
>>
>> Where things can go wrong is when:
>> - there is no explicit bond topology information in the file you read
>> - there is no "name" associated with the atoms or something that is not
>> equivalent to the element so the bond guess is wrong
>> - the list of covalent radii has no specific value for your elements and
>> thus VMD uses a default value (which may not be suitable)
>>
>> You can use atom selections to change names and radii as needed and then
>> issue the "mol bondsrecalc" command to redo the heuristics.
>> Or you figure out some other way to get the bond topology data and store
>> it in a suitable file (e.g. a .psf) file and load that before loading your
>> actual file.
>>
>> On Wed, Mar 30, 2022 at 9:08 AM maxim todoru <mtodoru_at_gmail.com> wrote:
>>
>>> Hi there,
>>> I performed a wave function analysis for some organic compounds, and I
>>> need to visualize the results, for that I used VMD, but I found that some
>>> C-H bonds don't show up. Is there the possibility to change bond length
>>> maximum in VMD in order to show the missing bonds ? I could use the
>>> "Topotools",  but it's tedious to pick a pair of atoms every time and add
>>> the bond, especially when the molecule is large.
>>> Just a note : I found the feature "Custom Bonding Parameters" in
>>> Gaussview program, which enables us to change the bond length limit between
>>> any two atoms in the periodic table, but Gaussview doesn't suit me in my
>>> work, especially in the visualisation.
>>>
>>>
>>
>> --
>> Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!ppk9OrMrZTJP1ZC1iPNxJIehZCfAkBY2HvIhFTVyfdObdQ3mYwoviS2fUmeFmSXsdQ$ 
>> <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!oPgQeI5z7a7Hvo8IAhSG0D2JuypOyUWCTH7f_x0dzeO7NJUANlTOLJSiE-g_Z8639w$>
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>