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Messages - omarove

Thank you for the answer, professor. I will check that out.
Thank you for your reply, Prof. Dubbeldam. Yes, the description for the RIGID_BOND is there and I can see how it is used in the examples. Yet, for the FIXED_BOND, which also has one input, it is not clear what is means and when it is used. I could only use it with flexible molecules. At least, I would want to know the concept of FIXED_BOND, does it imply that the bond length is fixed? The only description available in the manual is that it is used for bonds constraint using the 'SHAKE' and 'RATTLE'-algorithm.  ???
Output files / Error: malloc(): corrupted top size
July 12, 2021, 10:35:14 AM
Hi all,

When running charge equilibration for MIL-101, the error message (malloc(): corrupted top size) shows up after reading the CIF file (not immediately). It seems like an error related to C language. Is it because of the huge size of the framework? If so, how can I perform the Qeq on MIL-101? I would appreciate any input.

Hi all,

While defining a molecule, what is the difference in setting it as RIGID or FIXED? I have tried both (for CF3CH2F) and the simulation showed zero absolute adsoprtion for the RIGID_BOND, while the FIXED_BOND yielded some adsorption. Also, when setting the bond as HARMONIC_BOND, it runs the initialization cycles (1000) and equilibration cycles (5000), but it stops at the ~3600th cycle (out of 5000). The error message shows "no energy conservation in internal MC scheme". The number of cycles is definitely low (it is just to experiment the different types of bonds). Can anyone explain?