Isn't Mark's script outdated for this purpose? charmm forcefields specify epsilon and sigmas so you only need to convert them:
gromacs(sigma) = (charmm(Rmin/2)/10) * (2/(2^(1/6))) gromacs(epsilon) = charmm(eps) * 4.184 For 1-4 pair interactions, gromacs(sigma1,4 i,j) = (charmm(Rmin/2_1,4_i) + charmm(Rmin/2_1,4_j))/(2^1/6) gromacs(eps1,4 i,j) = sqrt(charmm(eps_1,4_i) * charmm(eps_1,4_j)) * 4.184 On 2012-10-15 07:27:51AM -0700, spin wrote: > Hello, everyone. > > I used the Mark's script's to convert the CGenff (version 2b7 ) parameter > file to Gromacs .itp files. In the ffcharmmnb.itp, the script gave the c6 > and c12, while the charmm's ffnonbond.itp showed epsilon and sigma.I do not > understand the relation between the c6/c12 and epsilon and sigma, and I > have a poor Perl skill. Can someone give me a solution? In addition, the > script makes all atoms' charge zero in the file, which is not the case in > the ffnonbond.itp. Why is it? > > Thank you! > > Qing Liu > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/The-problem-of-converting-CGenff-parameters-to-those-of-Gromacs-tp5002042.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
