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
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 ac
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