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 <[email protected]> > An: "[email protected]" <[email protected]> > 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 ; > THESE ARE 1-4 INTERACTIONS > > 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 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://www.gmx.net/de/go/freephone/ -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
