Dear All,
I’m trying to perform relative binding free energy calculations for the transformation from a neutral to a charged molecule. I know reading several articles that this kind of transformations are affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). Screening the letterature I found different corrections for ions but nothing for charged molecules. Can someone suggest me clear articles about that or help me to understand which kind of corrections should I use?
Thank you in advance for every kind of help.
Thank you Zhivko Asenov Velkov but I forgot to mention I use Molecular Dynamics simulations.
AlchemistryWiki is an excellent resource to help you with practical details of alchemical transformations in MD. The linked site (and probably other articles on that Wiki) should address exactly what you're looking for.
http://www.alchemistry.org/wiki/Charged_binding_calculations
The correction can be system/site-specific; it can be applied as a scaling factor to the calculated free energies. The scaling factor can be determined by comparing the calculated and experimental free energies; the latter should be obtained with the same or similar system/site.
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