I am writing my thesis on the functionalization of a single-walled carbon nanotube with Fmoc-AA structures in NAMD software. My system consists of (30,30) chirality SWNT and 150 Fmoc-AA structures. After the minimization step in 5000 steps, I am getting the following warning in the equilibration step (NPT simulations-10 ns).
**FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint, increase margin, or disable useFlexibleCell for liquid simulation.
I disabled Useflexiblecell, I increased the minimization step thinking that the structure was not minimized and I did not fix the CNT in npt simulations. However, npt simulation are not completed.
When I skip the equilibration step and go to the production step (simulation time is 200 ns, NVT ensemble), bubble nucleation formation was observed.
I thought it was related to pbcwrap, but it didn't work this command even though I wrote the script correctly. How can I fix bubble nucleation?
Dear Sıla Kılıç many thanks for asking this interesting technical question, for which I cannot really provide an expert answer because we are synthetic chemists. For handling the message "**FATAL ERROR: Periodic cell has become too small for original patch grid!" it might be worth having a look at the following potentially useful guide :
NAMD TUTORIAL
https://warwick.ac.uk/fac/sci/moac/degreescopy/degrees-copy/modules/ch926/workshop/namd-tutorial-win.pdf
(see attached pdf file)
I assume that you checked this already but, if not, it might be helpful.
I wish you good luck solving your problem and hopefully some expert answers to your question. With best wishes, Frank Edelmann
Dear Frank T. Edelmann ,
Thank you for your valuable reply. As you said, I have reviewed the tutorial in detail before. However, I will reconsider the tutorial on your suggestion.
Thank you for your best wishes, Sıla KILIÇ
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