Free-energy calculations - Theoretical Biophysics Group
Free-energy calculations - Theoretical Biophysics Group
Free-energy calculations - Theoretical Biophysics Group
You also want an ePaper? Increase the reach of your titles
YUMPU automatically turns print PDFs into web optimized ePapers that Google loves.
33 BEUTLER ET AL. (1994)<br />
34 ZACHARIAS ET AL. (1994)<br />
<strong>Free</strong>-<strong>energy</strong> perturbation <strong>calculations</strong> “Alchemical transformations”<br />
Solution: Modification of the parametrization of the van<br />
der Waals term in the potential <strong>energy</strong> function that governs<br />
the interaction of an appearing, or disappearing,<br />
atom, i, with an unaltered one, j: 33<br />
U vdW<br />
ij<br />
(rij; λ) = 4 ɛij λ n ×<br />
⎧<br />
⎪⎨<br />
1<br />
<br />
⎪⎩ αvdW (1 − λ) 2 62 rij<br />
+<br />
σij<br />
−<br />
1<br />
αvdW (1 − λ) 2 ⎪⎬<br />
6 rij<br />
+ ⎪⎭<br />
σij<br />
Or equivalently, 34<br />
U vdW ⎡⎛<br />
(rij; λ) = 4ɛij(1 − λ) ⎣⎝<br />
σ2 ij<br />
r2 ⎞6<br />
⎛<br />
⎠ − ⎝<br />
ij + αλ<br />
σ2 ij<br />
r2 ⎞3<br />
⎠<br />
ij + αλ<br />
⎤<br />
⎦<br />
Possibility to scale interactions with different schedules.<br />
Chris Chipot <strong>Free</strong>-<strong>energy</strong> <strong>calculations</strong><br />
⎫