make above files executable.
Make random rotation of a molecule as optional
For random rotation not collide, we may need very big box.
initial version of rest_lipid_top.py
it reads the lipids_43A1-S3.itp and creates the typeA and typeB for bonds, angles, dihedrals and etc.
The name conversion between typeA and typeB is simple for
	bonds g--> h
	pairs no change
	angles g --> h
	dihedrals g--> h

Name for atoms need more consideration
we want to the typeB name create from mapping from typeA does not collide with the existed names in the force field.
We need to check all the atom types in ffG43A1-S3par.02.itp to find out if our mapping is valid.

Desgn:
	rest_lipid_top.py  : read toplopy file from lipid.top
	rest_force_field_top.py : read force field both bonded and noboned parameters; for gromos 43a1-s3 , the bonded and nonbonded parameters are in the same file. This is the only format that is supported right now
lnx_util: add feature that output  the invalid input parameters
rest_force_field: read and parse force field parameters for rest. read both the bonded and nonbonded parameters
rest_lipid_top.py: read the solute topology files
rest_main.py   : main function to generate rest topology
output gamma in rest_main.py for easy check for users.
ignore tags
add new feature  to rest_lipid_top.py so that it can create individual topology for each lambda
add chi_square.py which calcuates the \chi value of form factors between experiments and simulations
exchange_stat calcualte the exchange rate from replica exchange log files
block_err.py : standard block average method to estimate std of mean
exchange_stat.py : compute replica exchange statistics from log file
replica_set_temperature.py : set replica exchange temperature according to trial temperatures. This may not work well.