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tsoc
openmm
Commits
8ae2ee1b
Commit
8ae2ee1b
authored
Oct 17, 2016
by
jchodera
Browse files
Update theory and API docs with correct dihedral range.
parent
0a1895d3
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docs-source/usersguide/theory.rst
docs-source/usersguide/theory.rst
+12
-11
openmmapi/include/openmm/CustomCompoundBondForce.h
openmmapi/include/openmm/CustomCompoundBondForce.h
+2
-1
openmmapi/include/openmm/CustomTorsionForce.h
openmmapi/include/openmm/CustomTorsionForce.h
+2
-2
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docs-source/usersguide/theory.rst
View file @
8ae2ee1b
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@@ -920,7 +920,8 @@ of four particles. That is, the interaction energy of each bond is given by
where *f*\ (\ *...*\ ) is a user defined mathematical expression. It may
depend on an arbitrary set of positions {\ :math:`x_i`\ }, distances {\ :math:`r_i`\ },
angles {\ :math:`\theta_i`\ }, and dihedral angles {\ :math:`\phi_i`\ }.
angles {\ :math:`\theta_i`\ }, and dihedral angles {\ :math:`\phi_i`\ }
guaranteed to be in the range [-π, π].
Each distance, angle, or dihedral is defined by specifying a sequence of
particles chosen from among the particles that make up the bond. A distance
...
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openmmapi/include/openmm/CustomCompoundBondForce.h
View file @
8ae2ee1b
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@@ -57,7 +57,8 @@ namespace OpenMM {
* <li>distance(p1, p2): the distance between particles p1 and p2 (where "p1" and "p2" may be replaced by the names
* of whichever particles you want to calculate the distance between).</li>
* <li>angle(p1, p2, p3): the angle formed by the three specified particles.</li>
* <li>dihedral(p1, p2, p3, p4): the dihedral angle formed by the four specified particles, in radians, on the domain [-pi,+pi).</li>
* <li>dihedral(p1, p2, p3, p4): the dihedral angle formed by the four specified particles, in radians, guaranteed
* to be in the range [-pi,+pi].</li>
* </ul>
*
* The expression also may involve tabulated functions, and may depend on arbitrary
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openmmapi/include/openmm/CustomTorsionForce.h
View file @
8ae2ee1b
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@@ -70,8 +70,8 @@ namespace OpenMM {
*
* Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
* functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.
* All trigonometric functions are defined in radians, with the torsion `theta`
on the domain [-pi, +pi), and log is the natural logarithm
.
* step(x) = 0 if x is less than 0, 1 otherwise. delta(x) = 1 if x is 0, 0 otherwise.
* All trigonometric functions are defined in radians, with the torsion `theta`
guranteed to be in the range [-pi,+pi]
.
*
log is the natural logarithm.
step(x) = 0 if x is less than 0, 1 otherwise. delta(x) = 1 if x is 0, 0 otherwise.
* select(x,y,z) = z if x = 0, y otherwise.
*/
...
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