dcd_file is the dcd trajectory file
pdb_file is the reference pdb 
dcd_file.rem contains the rem data of the dcd file
ref.pdb is the same trajectory in pdb; compare it with the new pdb

compile dcd2pdb in ../src:
gfortran dcd2pdb.f90 -o dcd2pdb

examples: 

1) extract a pdb from dcd_file using a reference pdb_file:
./dcd2pdb.bash pdb_file dcd_file > pdb;

2) extract frames from replica 1 from dcd_file using a reference pdb_file:
./dcd2pdb.bash pdb_file dcd_file 1 > pdb;





