[gmx-users] Conformation free energy

David Mobley dmobley at gmail.com
Wed Jun 7 00:29:54 CEST 2006

If you're just interested in the free energy of rotating a bond, I
would suggest umbrella sampling, as it's far more efficient for doing
that than doing the bond rotation alchemically, as you're suggesting.


On 6/3/06, esther <ecaballe at uoregon.edu> wrote:
> Hello,
> I am studying a protein that has an amino acid modeled as a two-state rotamer in the crystal structure. I would like to quantify the probability of each conformation, so I thought of doing a FEP calculation. As I haven't seen much about this in the mailing lists, save for a D- L- amino acid calculation, I am wondering if there is a more obvious way to do this that I've overlooked? And if there isn't, what is the path to go from conformation 'A' to conformation 'B' in the top file?
> Thanks in advance for your help,
> Esther
> Esther Caballero-Manrique
> Graduate Teaching Fellow
> Chemistry Department
> 1253 University of Oregon
> Eugene, OR 97403-1253
> (541) 346-2485
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