Difference between revisions of "OBForceFieldGhemical"

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=== Electrostatic ===
 
=== Electrostatic ===
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[[Category:Force_Fields]][[Category:Developer]]

Revision as of 10:47, 15 February 2007

OBForceFieldGhemical class

This class is an implementation of the molecular mechanics force field used in the Ghemical program. It is an all-atom method similar to the Tripos-5.2 force field.

Bond Stretching

BondEGhemical.png

E_{bond}=k_{b}(r_{ab}-r_{ab}^0)^2

k_b: bond stretching force constant (ghemical.prm)

r_{ab}^0: ideal bond length (ghemical.prm)

r_{ab}: bond length between atoms a and b

Angle Bending

AngleEGhemical.png

E_{angle}=k_a(\theta_{abc}-\theta_{abc}^0)^2

k_a: angle bending force constant (ghemical.prm)

\theta_{abc}^0: ideal angle (ghemical.prm)

\theta_{abc}: angle

Torsional

TorsionSingleEGhemical.png TorsionDoubleEGhemical.png

E_{torsion}=\frac{1}{2}V_t(1 + s_t cos(n_t \omega_{abcd}))

V_t: rotational barrier (ghemical.prm)

s_t: +1 if staggered minimum, -1 if eclipsed minimum (ghemical.prm)

n_t: multiplicity (ghemical.prm)

\omega_{abcd}: torsion angle

Van der Waals

VDWEGhemical.png

E_{vdw}=k_{ab}\left(\frac{1}{\sigma_{ab}^{12}} - \frac{2}{\sigma_{ab}^6}\right)

k_{ab} = \sqrt{k_a k_b}: force constant (ghemical.prm)

\sigma_{ab} = \frac{r_{ab}}{R_a + R_b}

R_a: vdw radius of atom a (ghemical.prm)

r_{ab}: separation (calulated in the same way as bondlengths)

Electrostatic