make derived classes/types
remove old code
allow multiple index groups to eaily be read in. need to fix gro function
fix errors when reading in 2 or more groups
add more cmd type functions
problem with reading in xtc file by itself
testing problem with reading in whole system when not specifying an index file. ok when specifying index file
fixed array bug in read_xtc. split up function
fixed output
make ndx class optional in init
comment out read gro section
add new new_vector routine
fix comments
make second argument for read_gmx
move gmx types to gmx mod
add new procedure to gmx class
add cmd procedures
eliminate need for cmd % create
fix cmd % get