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Incorrect Bond Angle in GUI Log Out | Topics | Search
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WebMO Support Forum » Bug Reports » WebMO Version 12.X » Incorrect Bond Angle in GUI « Previous Next »

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James Bialas
Unregistered guest
Posted on Wednesday, February 29, 2012 - 2:22 pm:   

Running a simple water molecule in NWChem via WebMO and the Molecule Viewer GUI is reporting an incorrect bond angle of 38.174 degrees while the raw output lists the correct 104.478 degree angle.

Any ideas on the cause of this discrepancy?
JR Schmidt
Moderator
Username: Schmidt

Post Number: 232
Registered: 11-2006
Posted on Wednesday, February 29, 2012 - 2:28 pm:   

Yes! My guess is that you are measuring the "wrong" bond angle, e.g. the O-H-H bond angle instead of the H-O-H angle. The order in which you select the atoms is important, and determines the measured angle.
pakamas tongcharoensirikul
Unregistered guest
Posted on Monday, March 12, 2012 - 12:50 pm:   

I am running the geometry optimization of formamide, and I got the bond angle of H-C=O equal to 109.5 which is a tetrahedral angle which is not correct; the bond angle of H-N-C is correct. I did measure it correctly; the geometry around C=O is not planar.
application/vnd.openxmlformats-officedocument.wordprocessingml.document.doc
formamide.docx (151.9 k)
JR Schmidt
Moderator
Username: Schmidt

Post Number: 234
Registered: 11-2006
Posted on Monday, March 12, 2012 - 12:53 pm:   

Send me the output file from Gaussian. WebMO only displays the results. If the geometry is incorrect, this means that either the initial geometry was poor or that the calculation was done incorrect.
pakamas tongcharoensirikul
Unregistered guest
Posted on Monday, March 12, 2012 - 10:07 pm:   

Thank you very much for replying. I am sending the output file. When I drew the structure, I used clean geometry, and it put C=O into a terahedral structure.
application/pdf.pdf
Raw Output - formamide.pdf (1493.7 k)
JR Schmidt
Moderator
Username: Schmidt

Post Number: 235
Registered: 11-2006
Posted on Monday, March 12, 2012 - 10:12 pm:   

There is no WebMO error. WebMO is correctly reporting the angle in the output file. You have not told Gaussian to optimize the geometry, so it is giving back the same tetrahedarl geometry you entered.
pakamas.tongcharoensirikul@gmail.com
Unregistered guest
Posted on Monday, March 12, 2012 - 10:35 pm:   

I redid again. I drew formamide without Hs, then I clean geometry, then add H. WEBMO makes N become trigonal planar which is not correct.
application/x-pdf.pdf
Print - 99922 - View Job.pdf (133.1 k)
pakamas.tongcharoensirikul@gmail.com
Unregistered guest
Posted on Monday, March 12, 2012 - 10:39 pm:   

I attached the wrong file. This is the correct file.
application/x-pdf.pdf
99948 - View Job.pdf (226.2 k)
pakamas.tongcharoensirikul@gmail.com
Unregistered guest
Posted on Wednesday, March 14, 2012 - 5:21 am:   

I am a high school chemistry teacher. If I have my students draw the structure and do the geometry optimization. I am counting on webmo giving the correct geometry. If I have to input the correct geometry at the start,then why do we have to do the geometry optimization. Beside the starting high school students will not know the correct geometry at the start; they rely on webmo giving them the correct geometry. Any comments
JR Schmidt
Moderator
Username: Schmidt

Post Number: 236
Registered: 11-2006
Posted on Wednesday, March 14, 2012 - 10:03 am:   

You did NOT do a geometry optimization. You did a "Single Point" / "Molecular Energy" calculation, which does NOT optimize the geometry.

To optimize the geometry, select "Geometry Optimization" from the calculation drop down list.
pakamas.tongcharoensirikul@gmail.com
Unregistered guest
Posted on Wednesday, March 14, 2012 - 3:34 pm:   

How do I setup for the geometry optimization, not single point calculation? Should I do the geometry optimization in MOPAC or GUASSIAN? It always seems like it is giving me different geometry each time I did the calculation. How can I become the registered user?
JR Schmidt
Moderator
Username: Schmidt

Post Number: 237
Registered: 11-2006
Posted on Wednesday, March 14, 2012 - 3:40 pm:   

I would suggesting spending a bit of time looking through the WebMO users guide, which should clear up many of this issues:
https://www.webmo.net/download/WebMO_Users_Guide.pdf

Note that the users guide is a bit dated (e.g. the screen shots are out of date), but nonetheless the basic concepts / procedures have not changed. This should address many of your questions regarding entering molecules, running basic calculations.

You may also find the book "Introduction to Computational Chemistry" by Jensen to be helpful for some basic idea.
pakamas.tongcharoensirikul@gmail.com
Unregistered guest
Posted on Wednesday, March 14, 2012 - 4:21 pm:   

Thank you for the suggestion. I already download the manual. The manual does have the calculation option of "single point calculation," but the current webmo that I am using now does not have the single point calculation. It does have the geometry optimization. SO when I do the geometry optimization, will it give me the best structure, and how will I know that?
JR Schmidt
Moderator
Username: Schmidt

Post Number: 238
Registered: 11-2006
Posted on Thursday, March 15, 2012 - 1:35 pm:   

Single Point / Molecular energy are synonymous. A geometry optimization will give the the "best" geometry.

If you are using WebMO through U. Illinois / NCSA, I would strong recommend talking with those folks for some guidance regarding the computations (or looking at the book I mentioned above). This forum is primarily for TECHNICAL assistance, and we are not able to provide detailed guidance to individual users due to time constraints.

You might also contact the Shodor Foundation (http://www.shodor.org/), who are a national resource for computational tools for education, including high school.

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