Initial commit
DRR - configure script, test commit.
Add preamble.
Add real README
Merge branch 'master' of https://github.com/mojyt/cpptraj

Conflicts:
	LICENSE
Add a markdown copy of README.
Improved markdown syntax.
Remove stray comma.
Add initial tests.
Add initial Travis-CI configuration file.
Modify Makefiles and scripts for standalone operation. Clean up extra test files. Add files required for LIE test.
Merge branch 'master' of https://github.com/mojyt/cpptraj
Add citation for SPAM. Add available memory calc.
Add Gaussian form to curve fitting. Fix up data set naming with multihist. Improve generation of default data set names.
Wrapper around Summary() function since not all distros default to bash.
Multiple changes from Amber GIT:
-Keep track of individual native contact stats in nativecontacts, including optionally time series. Combine some common functionality into macros. Contacts are now stored using map instead of set for efficiency.
-Split contacts map into native and non-native contacts, which is much easier to read.
-Add ifdef for systems that do not support _SC_XXX variables for sysconf().
-Add code to determine the available (free) memory on a Mac.
-Add normframe and normdensity options to grid for normalizing by # frames or # frames and specified molecule density respectively. Add function to GridBin for calculating voxel volume.
-Frame::Center -> Frame::CenterAtoms to avoid confusion with other routines.
-Fix autoimage centering to box center for general triclinic cells.
-Use CenterOnOrigin instead of CenterAtoms, latter is overkill.
-New boxcenter function in vector.
-Update test for fixed triclinic autoimaging.
-Move centering functionality back to Action_Center since nothing else needed it.Get rid of obsolete enumerated type for centering in Frame and corresponding unneeded code in Action_Autoimage.
Fix permissions.
Update test output for fixed autoimage centering.
Some changes that will hopefully make the Travis-CI build work.
Add missing arpack dependency.