* Version 0.6.3 (Jun. 17, 2013)
 ** molx for Amber topology files in charmm format
   add option in molx for Amber toplogy files in charmm format
   e.g., in molx input file, 
   mdat_amber on

 ** optimized influence function
   In PME, optimized influence function improves accracy of 
   reciprocal energy and forces.
   e.g., in marble control file,
   [ewald]
     opt_infl_func = on

 ** long range LJ terms
   Now, only 1/r^6 terms are calculated in accordance with amber

 ** Non zero total charges
   In the case of non zero total charges of system, an energy term of 
   uniform neutralizing plasma was added in PME.
   If you omit this term as in the previous version, specify the option 
   in control file as,
   [ewald]
     uniform_neutralizing_plasma = off
   In default, uniform_neutralizing_plasma is on.

 ** pontential type for RMSD restraint
   Pontential types for RMSD restraint can be changed.
   [restraint]
      method = rmsd
      potential_type = upper
     -> if rmsd > rmsd0, E = (rmsd-rmsd0)^2
        if rmsd < rmsd0, E = 0

      potential_type = lower
     -> if rmsd < rmsd0, E = (rmsd-rmsd0)^2
        if rmsd > rmsd0, E = 0

      potential_type = normal (default)
     -> = (rmsd-rmsd0)^2


 ** k_per_atom for RMSD restraint
   k = k_per_atom * N_atom
      
* Version 0.6.2  (Oct. 31, 2012)
 ** x dimension of pe array
   Correct communication routines when the x dimension of 
   the PE array is 1 and the y dimention is more than 1.
 
 ** MBL_NPX
   Add envionment variable MBL_NPX for dimensions of PE array.
   e.g., export MBL_NPX="1 2 3" 

* Version 0.6.1  (Oct. 18, 2012)
 ** OMP_NUM_THREADS = 1
   Corrected PME routine when the number of threads equals 1.

 ** Update trajectory output
   owing trajectory output 

   amber type trajectory
   [md]
     trj_file = file.trj      #  trajectory file name
     trj_output = XB          #  Output coordinates and box info
     trj_amber_boundary = on  #  box info of amber type
     trj_wrap_molecules = on  #  coordinates are wrapped into primary box
     trj_step = 100           #  trajectory output step

   Example VMD command: vmd start.pdb -crdbox file.trj

   dcd file
   [md]
     trj_file = file.dcd      #  trajectory file name
     trj_format = dcd         #  DCD type
     trj_output = XB          #  Output coordinates and box info
     trj_wrap_molecules = on  #  coordinates are wrapped into primary box
     trj_step = 100           #  trajectory output step

   Example VMD command: vmd start.pdb -dcd file.dcd
   Box info is included in the dcd file.

   dcd + xst 
   [md]
     trj_file = file.dcd      #  trajectory file name
     trj_format = dcd         #  boundary info of amber type
     trj_output = XB          #  Output coordinates and box info
     trj_xst_output = on      #  xst file (file.xst) is also outputted.
     trj_wrap_molecules = on  #  coordinates are wrapped into primary box
     trj_step = 100           #  trajectory output step

   Example VMD command: vmd start.pdb -dcd file.dcd
   File file.xst is also output. 

* Version 0.6.0  (Sep. 30, 2012)
 ** marble release under GPL licence
