Simulate lipid bilayer with a systematically solvent-free coarse-grained model
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configs/examples
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srcmembrane
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README.md
cgtoolsmain.tcl
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run_Espresso.mpi

README.md

CGTools

An ESPResSo-compatible software for implementing simulations of lipid membranes with 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 acknowledge the author(s) if you use this code in any way.

Quick start

CGTools 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 ran.

PLEASE CITE US!

If you use CGTools and obtain scientific results that you publish, we would ask you to acknowledge the usage of CGTools by referencing

[1] Z.-J. Wang, M. Deserno. A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations. Journal of Physical Chemistry B, 2010, 114(34): 11207-11220.

[2] 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.

General information

Portal: http://www.wiomax.com/cgtools E-MAIL: info@wiomax.com