I am working on abalone software and I tried running the MD of cyclodextrin and nitrophenol.As soon as I start the MD,nitrophenol gets deformed.How to solve this problem?
I did.i also optimised the structure through NWChem,after optimisation is remains planar but as soon as i add beta-cyclodextrin and start MD,nitrophenol gets deformed.
It will also be important that which basis sets you used while optimizing as nitrophenol contains lone pairs and I think you might have to use diffused basis sets.
I tried to make p-nitrophenol in Abalone. It looks good. What do you mean - "deformed"?
http://www.biomolecular-modeling.com/Abalone/index.html
It deformed into a non planar structure.Can you please share the details about how you constructed it in abalone
I opened the panel "Draw", chose benzene kernel, replace two hydrogen by OH and NO2 (double bonds) and optimized. I see a flat geometry. Calculated partial charges. Optimized again. Geometry is flat.
i did the same but when i tried running the dynamics with cyclodextrin ,its(nitrophenol) geometry turned non planar
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