Release_note

This is the second version of Upside.
It's still in the alpha stage. It will be updated or corrected continuously.

Changes:

   for users

       1. support the latest ff2.1 and membrane protein force fields. NOT compatible with ff1.0, ff1.5 and zongan's  membrane force field

       2. switch to python 3

       3. trans-cis PRO simulation (will add example to show)

       4. the config process is divided into basic stage and advanced stage, which are completed by upside_config.py and advanced_config.py respectively.

       5. you don't need the ugly_hack_break_chain.py any more. When the system has multiple chains, the script will handle it automatically.

       6. replica exchange. When you have multiple swap-sets, the exchange attempts of differet swap-sets are set to be handled asynchronously. 
          For example, if you set the --replica-interval as 5, the swap-set1 and swap-set2 will try to exchange at time 5,15,25... and 10,20,30... respectively. 
          It is helpful for short-term simulations (such as training). It also means that you need to halve the --replica-interval value to maintain the 
          same exchange frequency as before.
       
       7. More flexible restraints. You have the opportunity to add special force just by modifying the python code, including but not limited to:
              pulls a group of atoms instead of just one atoms
              rotate four atoms or groups
              add walls to confine the motion of any atoms/groups in arbitrary dimensions, etc.
          I will add examples to show more
       
       8. examples. Above changes are big. But don't worry, I've created an example folder that contains the most commonly used simulation scenarios. 
          These examples will continue to be added or improved. Please try and give suggestions or requests.

       9. add intensive memory mode

       10. add multi-step integrator

    for developers

        1. abstract as many CoordNodes and PotentialNodes as possible so that developers can flexibly implement new forces at the python level

        2. added upside_node library to manage CoordNode and PotentialNode

        3. cleaned upside_config.py, leaving only the core functions. Add a advanced_config.py to deal with various forces such as RMSD restraint, 
           pulling simulation, etc. 

        4, clean up C++ code (in progress)