[gmx-users] Lennard-Jones Parameters in ffnonbonded.itp

lloyd riggs lloyd.riggs at gmx.ch
Mon Feb 20 20:22:51 CET 2012

A quick answer to this is, there's two sets of tables based on equations I know of off hand for LJ's and calculating the other such LJ parameters from these.  In one it uses the epsilon/ sigma and the other a table of either the 9-6 or the 6-12.  The later two you can look up either on the European or US standards data base on the web or in a CRC book.  The former, you have to do a conversion, although for your force field you might have to do a back conversion if you look up say the 6-12.  I would trust A professor more with this though...and getting the proper equations.  With the equation you have listed below it would be strait forward plug and paste and then a calculator...either you have one or the other portions of the equation.  I assume the 4 epsilon is from the normal equation, and the sigma as well for a 12-6 equation.  All of these are on wiki though as well.

Hope thats not too confusing.

Stephan Watkins

-------- Original-Nachricht --------
> Datum: Mon, 20 Feb 2012 17:36:07 +0000 (GMT)
> Von: Lara Bunte <lara.bunte at yahoo.de>
> An: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Betreff: [gmx-users] Lennard-Jones Parameters in ffnonbonded.itp

> Hello
> I use a charmm force field in gromacs. I almost finished my
> parametrization except for Lennard-Jones parameters. For this parameters I want to adopt
> the values in the charmm force field for the basic atom types. 
> In gromacs I have to put this parameters in the ffnonbonded.itp file in
> the section [ pairtypes ] and I have to give following informations: 
> ; i     j       func    sigma1-4        epsilon1-4 ;
> in example
> CP1     CP1     1       0.338541512893  0.04184
> Now here is a section of information given in the charmm documentation. 
> !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
> !
> !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
> !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
> !
> !atom  ignored    epsilon      Rmin/2   ignored  
> eps,1-4       Rmin/2,1-4
> !
> HN1      0.0       -0.0460    0.2245 
> HN2      0.0       -0.0460    0.2245 
> The question is: 
> How to adopt the values in the charmm force field for the basic atom types
> in gromacs? I do not really know what I have to write in the [ pairtypes ]
> section in gromacs. 
> Thank you for helping me
> Greetings
> Lara
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