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.
David
On 6/3/06, esther <[EMAIL PROTECTED]> 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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