Do you want to calculate the absolute energy difference of these two
conformations or free energy difference?
Ilyas Yildirim, Ph.D.
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On Thu, 28 Jun 2012, Steven M. Graham wrote:
> I'm re-posting this as I got only one response (thanks Jiri; see below). Not a criticism - I know if I don't respond right away the post tends to get lost in my inbox.
>
> I'm going on the assumption that there are no 'silly questions'...
>
> How would one calculate the energy difference between a north conformation and a south conformation of a nucleoside in solution? Clearly, one could build a periodic box of H2O for each structure and optimize, but wouldn't the water energy dominate? One could delete the water molecules, but now that's a vacuum calculation. Let's assume using a distance-dependent dielectric is not going to give realistic values. Perhaps a solvent model, like GB or PB?
>
> Jiri: Read your chi(OL) paper - I was already familiar with it. The problem in I want the N/S energy difference at the minima, which you've set to zero to compare the chi torsion profiles and chi dihedral terms. But thanks anyway.
>
>
> Steven M. Graham. Ph.D.
> Associate Professor
> Department of Chemistry
> St. John's University
> 8000 Utopia Parkway
> Queens, NY 11439
> 718-990-5217
> grahams.stjohns.edu
>
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Received on Thu Jun 28 2012 - 15:30:02 PDT
