GitLab

Fixed error in DrudeForce::updateParametersInContext()

Support new 12-6-4 potential

Fix customnonbondedforce segfault

are changed for CustomNonbondedForce.

- Don't make a Copy method on FunctionInfo
- Have the Copy() methods on the TabulatedFunction subclasses return a pointer

necessitated creating a Copy method to do that on TabulatedFunction classes.

segfaults when you use the long-range dispersion correction with the
CustomNonbondedForce if the force uses TabulatedFunction objects. Basically, it
prevents the copy from taking ownership (and deleting) the functions in its
destructor.

The use cases for CustomNonbondedForce copying currently is to recompute the
long-range prefactor if the parameters change (so the CustomNonbondedForceImpl
kernels need a copy of the Force object). Doing a full (deep) copy would be a
bit slower (although would only need to be paid once for each
CustomNonbondedForce object being used).

Fixed a bug in unit conversion for sequences

Convert AmberInpcrdFile data structures from lists to Vec3

- Convert coordinates, velocities, and box vectors into Vec3 objects to avoid a
  subtle bug in the units module with respect to silently modifying mutable
  collections in-place when converting to a new set of units.

Fixed bug when running on a CPU device

Revert to older Travis-CI testing framework to separate testing from conda dev builds

Implemented CHARMM polarizable force field

Depressing compromise to make the ordering of atoms in improper torsions as consistent as possible with both AMBER and CHARMM

Update default long-range option and expand test

added.

correction by default. Then add a test for using the long-range correction and
_not_ using the long-range correction.  Comment out the test using the
long-range correction since it currently segfaults.  When the fix for the
segfault is added, this test can be reinstated (but the energy has to be
updated)

This change in default makes it consistent with the default behavior for the
classical NonbondedForce, and I would have set that as the default to begin with
if I had known it was supposed to work.

Updated long range correction code to work with new style tabulated functions

Fix error reporting in a corner case.  Looks like a case of incomplete copy-and-paste...

Add support for Amber prmtop files with NBFIX

copy-and-paste...

TestAmberPrmtopFile.py tests take 17 seconds combined on my laptop).

force field utilizes nbfix functionality. Without this commit, using a ff14IPQ
topology file (or one modified by ParmEd to contain off-diagonal LJ elements),
would happily run, but ignore off-diagonal elements.

The new Chen and Garcia RNA force field (see doi:10.1073/pnas.1309392110) also
utilizes off-diagonal terms in its parametrization scheme.

One shortcoming is that the approach taken here -- using a pair parameter lookup
table -- cannot be currently used with a long-range correction because it is not
a `Continuous1DFunction' by virtue of using two `Discrete2DFunction'
TabulatedFunction classes.

Energies here match the values obtained with Amber to 0.01 -- 0.1 kcal/mol
(within 0.1% of the total).