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Given an input parameters for the MARTINI force field such as:

;;;;;; HYDRATED CHLORIDE ION

[moleculetype]
; molname   nrexcl
  CL-       1

[atoms]
;id     type    resnr   residu  atom    cgnr    charge
 1  Qa  1   ION     CL-     1   -1.0 

I wish to know which parameters go into which term in the equation.

I'm after the either the source code of the MARTINI force field, or just the equation. I believe that it's just a combination of 12-6 LJ and electrostatic interatction, but I want to make sure.

Thanks

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  • $\begingroup$ These are input parameters for which MD program? $\endgroup$ – Bill Barth Oct 14 '13 at 11:49
  • $\begingroup$ These are the input parameters given on the MARTINI website. I suppose that they are suppose to work with any program that implements MARTINI. $\endgroup$ – RNs_Ghost Oct 14 '13 at 12:05
  • $\begingroup$ Maybe the papers on their about page will point you in the right direction: md.chem.rug.nl/cgmartini/index.php/about $\endgroup$ – Bill Barth Oct 14 '13 at 13:14
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    $\begingroup$ Why is it that no one in the MD community wants to teach people how to actually write useful MD code? $\endgroup$ – RNs_Ghost Oct 14 '13 at 14:56
  • $\begingroup$ Well, I'm not in the MD community, but the typical place to go to find out what is being done in the world is directly to the source. I'm assuming that the top couple of survey papers on the authors site might be helpful. Have you read them? $\endgroup$ – Bill Barth Oct 14 '13 at 15:52
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That file is input for GROMACS, which the Martini http://md.chem.rug.nl/cgmartini/index.php/faq hints was the software with which the reference implementation was developed. The Martini http://md.chem.rug.nl/cgmartini/index.php/tutorial page also suggests GROMACS.

The Qa atom type is defined elsewhere by the forcefield files. You can read about the file formats and the equations whose parameters they describe in the GROMACS http://www.gromacs.org/Documentation/Manual.

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