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Cyclohexane torsions #14

Open ramess101 opened 5 years ago

ramess101 commented 5 years ago

@jpotoff @msoroush

We have discussed this previously in Issue #8 . The question is how/where do we want to address the use of n-alkane torsions for cyclohexane?

I have moved most of the bonded parameter discussion to supporting information, according to the JCED MMS guidelines:

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So now I am not sure if we want to include the statement about TraPPE cyclohexane torsions in the manuscript or in the supporting information. If we put it in the supporting information it is much less likely that this error will be corrected and it is quite likely that future practitioners will continue to use the wrong parameters. So maybe we should include it in the manuscript. However, if we are trying not to offend Siepmann the SI might be a better spot.

I think we should include it in the manuscript but be very careful how we word it. The current version is probably still too harsh, so I would appreciate any additional feedback.

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msoroush commented 5 years ago

@ramess101 I am sorry, I am not a good politician. @jpotoff would be more helpful in this area.

ramess101 commented 5 years ago

@msoroush @jpotoff

I think the torsion issue has been solved. The equation on the TraPPE website now shows:

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I also found the same equation in the TAMie publication for cyclohexane:

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What do we want to do about this? I think we need to modify our statement to mention that the equation on the TraPPE website has been corrected, right?

jpotoff commented 5 years ago

@ramess101 Sure, mention the error in the paper, but state that the website has the corrected value.

ramess101 commented 5 years ago

@jpotoff @msoroush

This is the updated discussion on the cyclohexane torsional potential. Let me know if you have any concerns:

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ramess101 commented 5 years ago

@jpotoff @msoroush

In Issue #26 @msoroush demonstrates that even with the alternative equation the torsional potential is wrong. So there might still be a missing negative sign for the c1 term. I have modified the explanation accordingly:

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