VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Thu Mar 23 2023 - 13:45:28 CDT

Hi JC thank you so much for your kind update, success👍🙂🚀

On Thu, Mar 23, 2023 at 2:29 PM Gumbart, JC <gumbart_at_physics.gatech.edu>
wrote:

> The red D indicates they are not displayed. Double-click it to turn them
> on.
>
> Best,
> JC
>
> On Mar 23, 2023, at 1:08 PM, Joel Subach <mjsubach_at_alumni.ncsu.edu> wrote:
>
> Hello JC thank you for your kind update and all the proper molecules are
> displayed but the water(s) (see screenshot).
> I also expanded the screen and there was no water(s).
>
> Thanks:)
> Joel 🚀
>
> On Thu, Mar 23, 2023 at 11:50 AM Gumbart, JC <gumbart_at_physics.gatech.edu>
> wrote:
>
>> Check which molecules are displayed in the VMD main window. It might be
>> off by default when loaded.
>>
>> Best,
>> JC
>>
>> On Mar 23, 2023, at 10:50 AM, Joel Subach <mjsubach_at_alumni.ncsu.edu>
>> wrote:
>>
>> Hello JC thank you for your kind update:).
>>
>> Yes, this procedure that you indicated is exactly what I input but the
>> water molecule(s) did not appear in my VMD visual,
>> just the ethanol (see-screenshot labeled gau). Whereas the second log
>> visualization via the Log QM Output File appropriately
>> visualized the final water interaction (see-screenshot labeled log).
>>
>> On Wed, Mar 22, 2023 at 5:40 PM Gumbart, JC <gumbart_at_physics.gatech.edu>
>> wrote:
>>
>>> Hi Joel,
>>>
>>> In the water interaction tab, there is a “load QM input files” button at
>>> the bottom - is that what you are referring to? That works for me at
>>> least. If it doesn’t for you, can you describe what happens when you try
>>> it?
>>>
>>> Best,
>>> JC
>>>
>>> On Mar 17, 2023, at 5:04 PM, Joel Subach <mjsubach_at_alumni.ncsu.edu>
>>> wrote:
>>>
>>> ...and moreover I also tried to load the water interaction input (GAU)
>>> files into VMD via the Load GAU Files button
>>> within the Water Int. tab of the ffTK GUI and this also did not promote
>>> visualization via VMD?
>>>
>>> Thanks if you can help since I would like to superimpose these gau image
>>> files with the parmetized log file images
>>> to visualize the water interaction optimization.
>>>
>>> On Thu, Mar 16, 2023 at 3:51 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
>>> wrote:
>>>
>>>> Hello I am working through the ffTK Tutorial 4 Charge Optimization and
>>>> successfully
>>>> generated my .gau files (page-17 from below Tutorial Link). There is
>>>> no gau
>>>> selection within the VMD visualization tab `Determine File Type´ not
>>>> enabling me to
>>>> visualize my several .gau files and the selection Automatically only
>>>> generates `Please
>>>> Select a File Type´ (see-attached screenshot).
>>>>
>>>> Is there a way for me to still visualize my .gau files via VMD?
>>>> Thanks:)
>>>>
>>>> *http://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf
>>>> <http://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf>*
>>>>
>>>
>>> <gau.png><log.png>
>>
>>
>> <Screenshot 2023-03-23 at 1.07.31 PM.png>
>
>
>