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cgtoolsmain.tcl
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run_Espresso
run_Espresso.mpi

README

CGTools-MP
=============================================================================================
CGTools-MP is an ESPResSo-compatible software for implementing simulations of lipid membranes
interacting with peptides or proteins using the systematically coarse-grained solvent-free 
model for quantitative phospholipid bilayer. 

License description
See the [Creative Commons Non-Commercial License 3.0] 
(https://creativecommons.org/licenses/by-nc/3.0/us/) for more details.


PLEASE CITE US!
=============================================================================================
If you use CGTools-MP and obtain scientific results that you publish, we would ask you to 
acknowledge the usage of CGTools-MP by referencing

[1] Z.-J. Wang, M. Deserno. Systematic implicit solvent coarse-graining
of bilayer membranes: lipid and phase transferability of the force field.
New Journal of Physics, 2010, 12(9): 095004.

[2] T. Bereau, Z.-J. Wang, M. Deserno. More than the sum of its parts:
Coarse-grained peptide-lipid interactions from a simple cross-parametrization.
The Journal of chemical physics, 2014, 140(11): 115101.


Quick start
=============================================================================================
CGTools-MP will *not* run unless a configuration file is specified in argument.
The main script should be parsed inside Espresso : 

   > Espresso cgtoolsmain.tcl <CONFIG_FILE> 
	      [-new]
	      [-replica [-connect HOST]]
	      [-annealing]
	      [-annealfast]

   where the brackets represent optional choices. 

   '-new' starts a new computation by deleting the existing folder if there is
   any, without this choice, the simulation will resume from the last checkpoint.

   '-replica' starts a parallel tempering simulation host. The different
   simulation temperatures are parameterized in the CONFIG_FILE. Adding the
   '-connect HOST' argument is required for slaves to connect to the host.

   '-annealing' starts an annealing simulation.

   '-annealfast' starts a fast annealing process, afterwards equilibrium the system 
   at the end temperature.

   Note that the optional arguments can be alternated, and they do not require
   brackets. 

At the end, the script will have created a new directory with stored configuration 
files inside.

The 'configs/' folder contains several configuration files that are ready to be run.

General information
=============================================================================================
CGTools-MP was developed by Zunjing Wang in 2008-2014
Portal: http://www.wiomax.com/cgtoolsmp
E-MAIL: info@wiomax.com