The files in this directory are used to create the "martini.lt" file
(containing MARTINI force field parameters for moltemplate).
These .PRM files are distributed with "EMC" written by Pieter J. in 't Veld.
The original MARTINI files are distributed at http://cgmartini.nl

Conversion from EMC (.PRM) format to moltemplate (.LT) format was 
done using the "emcprm2lt.py" script written by David Stelter.
Here is an example how to use the emcprm2lt.py script:
--------------------------------
Step 1:
../convert_EMC_files_to_LT_files/emcprm2lt.py martini.prm lipids.prm ions.prm cholesterol.prm --bond-style=harmonic --angle-style=cosine/squared --pair-style=lj/gromacs/coul/gromacs --name=martini
--------------------------------
Step 2:
The MARTINI force field uses custom "special_bonds" settings and 
electrostatics settings.  We must override the "pair_style" and "special_bonds" commands,
as well as customize the relative dielectric constant.

echo 'MARTINI { # append overriding settings to the force field' >> martini.lt
echo '  write_once("In Init"){' >> martini.lt
echo '    pair_style hybrid lj/gromacs/coul/gromacs 9 12 0.000001 12' >> martini.lt
echo '    special_bonds lj/coul 0.0 1.0 1.0' >> martini.lt
echo '    dielectric 15.0' >> martini.lt
echo '  }' >> martini.lt
echo '}' >> martini.lt
--------------------------------

This will generate a file named "martini.lt" which (in this example)
only includes the force field parameters for lipids, ions, and cholestrol.
Later you can define new molecules in moltemplate using:

import "martini.lt"
NewMolecule inherits MARTINI {
  write("Data Atoms") {...atom coordinates and types go here...}
  write("Data Bond List") {...list of bonds goes here...}
}

See "DOPC.lt" in /examples/coarse_grained/MARTINI_examples/ for more details.

(Note: The rigid bond constraints used for cholesterol in the original MARTINI
 model for cholesterol have been replaced by stiff but flexible bonds.
 There is a trade-off between increasing the stiffness of the bonds
 and using larger time steps.  To alter the stiffness of the bonds
 edit the "ITEM	BOND" section of the "cholesterol.prm", edit the "k"
 parameters (3rd column, for the "S..." entries, and run "emcprm2lt.py" again.)

---- Credits: ----
emcprm2lt.py was written by David Stelter
EMC was written by Pieter J. in 't Veld
MARTINI was created by S.J. Marrink and coworkers (http://cgmartini.nl)

---- additional citation request ----

Since we borrowed force field parameters from files distributed with EMC,
if you use files generated by "emcprm2lt.py", please also cite the EMC paper:
P. J. in ‘t Veld and G. C. Rutledge, Macromolecules 2003, 36, 7358


