GitLab

Update from upstream

WIP: Nosé-Hoover Thermostat

Lipid

The following lipid were added to the addMembrane() method: DLPC,
DLPE, DMPC, DOPC, DPPC.

Original pdb files were taken from
http://www.fos.su.se/~sasha/SLipids/Downloads.html .

Original files were obtained at temperatures between 293K and 303K.
NPT MD simulations were run for all the systems at 298K for ~10 ns
and the last simulation  step was used to create the pdb files.

Fix Lepton optimization with -ffast-math

Lepton::ParsedExpression::getConstantValue() used to return NaN to indicate non-constant
expressions. This can break with -ffast-math optimization where NaN comparisons are
not defined.

This patch defines bool isConstant() to test whether an expression is constant before
calling getConstantValue(). getConstantValue() now throws an exception if called on a
non-constant expression.

Fixed a potential bug in charmmpsffile parser when building 1-3 and 1-4 exclusions

Update from upstream

Signature modification to Modeller.addExtraParticles()

Within Modeller.addExtraParticles(), add the ability to pass down
an option to modify compiled.matchResidueToTemplate() 's
ignoreExternalBonds parameter.

https://simtk.org/plugins/phpBB/viewtopicPhpbb.php?f=161&t=11264&p=0&start=0&view=&sid=e384beeb08f3bfd767dcfb546006ad63

Optimized processing of expressions with tabulated functions

ThreeParticleAverageSite Doxygen fix #2473

Update travis to test more recent Python versions

runForClockTime() updates currentStep correctly

Get and scale velocities using numpy during simulated tempering

Improved determination of elements from Gromacs top files