It pains me to say this, but I am not 100% certain of your terminology. Free energy difference is, of course, delta G, and would thus include the entropy of the north/south change. 'Absolute energy difference' is...just delta H? What I want, at the end of the day, is the equilibrium ratio of the solvated north/south conformers to compare to in vacuo values.
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
-----Original Message-----
From: Ilyas Yildirim [mailto:i-yildirim.northwestern.edu]
Sent: Thursday, June 28, 2012 6:26 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Re [amber] north/sout energy difference
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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jun 29 2012 - 10:30:02 PDT
