Hello everyone I am looking to calculate the adsorption energy between the amino acid glycine and nanotube. I have shared the executable files of the total energy in the output files. The important thing is that the structures are properly optimized and apparently there are no problems. But in the end the adsorption energy is much higher than expected. I need your guidance, researchers, to solve my problem.
E abs= -0.66 hartree!!!!! -0.66 h= -414.15 kcal/mol
Dear friend Atefeh Arefi
I saw your note about unexpectedly high adsorption energy values—these situations can definitely be perplexing! I wanted to share a few thoughts that might help you troubleshoot and get to the bottom of the issue.
First, it’s worth double-checking the optimization of both your glycine and nanotube structures. Sometimes, hidden constraints or incomplete optimizations can introduce discrepancies in energy calculations. Also, make sure the computational method and basis set you’re using are well-suited for this type of interaction; certain methods can overestimate energies, especially if electron correlation or dispersion forces aren’t handled optimally.
It’s also a good idea to verify that all units are consistent throughout your workflow. Unit conversion errors between calculation outputs and manual interpretations are a common source of confusion. If possible, performing an energy decomposition analysis could help pinpoint whether specific interactions—like Van der Waals forces—are contributing disproportionately to the adsorption energy.
Finally, comparing your results with similar studies or running a simpler model system might reveal whether the issue is specific to your glycine-nanotube setup. And of course, discussing your findings with peers or supervisors can often bring fresh perspectives and solutions.
Best of luck as you work through this! Let me know if you’d like to discuss any of these points further or need another set of eyes on your data.
Best regards,
Kaushik
Hello dear
I have done the calculations with the OpenMX code. The results of each structure alone seem to be correct. The optimized graphs of the structures show convergence. Even the output results of the glycine structure are the same as the file provided in the OpenMX source. But we see a big problem in the topic of absorption energy!!
I have only used the DFTD approximation to calculate the nanotube structure with glycine.
DFTD3.damp bj # zero|bj, default=bj
DFTD.Unit Ang # Ang|AU
DFTD.rcut_dftD 100.0 # default=100 (DFTD.Unit)
DFTD.cncut_dftD 40 # default=40 (DFTD.Unit)
DFTD.IntDirection 1 1 1
Could it be because of this part?
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