Re: [gmx-users] Gromos parameters for atom type OA
Hi, slightly off-thread, I'd like to add that the oxygen parameters of 53a6 have been recently refined in a new set called 53a6OXY (http://pubs.acs.org/doi/abs/10.1021/ct1006407). So this ends up in new values for LJ and charges for the OA atom (as well as for other oxygen atoms). Cheers, Patrick Le 09/12/2011 20:03, Javier Cerezo a écrit : GROMOS force field builds the LJ parameters by multiplication of the square-rooted parameters per atom type (hence the SQRT(C6) and SQRT(C12) labels). In the case of the repulsion term (C12), up to three of such parameters are possible: SQRT(C12(1)) SQRT(C12(2)) SQRT(C12(3)), when combined with other atoms, depending on the desired repulsion strength (e.g. the enhanced C12(3) repulsion is used to keep charged groups separated). Which of the three is used depends on the combination of atoms, and is specified in an (asymmetric) matrix (see pages 14 and 15 in the pdf pages of 45a3 and 54a6 force fields from the GROMOS site, or in the ifp file the last lines for each atom type containing 1, 2 and 3). For the case of OA, this matrix specifies that the second C12 term is to be used when OA encountes another OA. So, according, to the ifp line you showed: C12(OA-OA) = SQRT(C12(2))_OA * SQRT(C12(2))_OA = 1.227E-3 * 1.227E-3 = 1.50553E-6 Which is the same for 45a3 and 54a6 force fields. Differences in the parameters will show up only in the cases where the SQRT(C12(1)) term for OA is to be used (e.g C12(OA-CH2)) Javier El 09/12/11 16:12, Samuli Ollila escribió: Dear all, I was comparing Gromos 45a3 and 53a6 force fields and I found something which I cannot understand. The atom type OA is described in ffG45a3nb.itp as: ;name at.num mass charge ptype c6 c12 OA 8 0.000 0.000 A 0.0022619536 1.505529e-06 and in ffG53a6nb.itp: OA 8 0.000 0.000 A 0.0022619536 1.505529e-06 which are same parameters. However, according to Gromos developers the atom type OA has been changed between Gromos 45a3 and 53a6. The parameters given by Gromos developers for 45a3 are # IAC TYPE SQRT(C6) SQRT(C12(1)) SQRT(C12(2)) SQRT(C12(3)) 3 OA 0.04756 1.1250E-3 1.227E-3 0.0 and for 53a6 3 OA 0.04756 1.100E-3 1.227E-3 0.0 The actual numbers are different for parameters used in Gromacs since the way to write parameters is different. My problem is that there is difference in OA type between 45a3 and 53a6 in parameters given by Gromos developers but not in the files distributed in Gromacs package. Can someone explain this? BR, Samuli Ollila -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- ___ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- gmx-users mailing listgmx-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
[gmx-users] Gromos parameters for atom type OA
Dear all, I was comparing Gromos 45a3 and 53a6 force fields and I found something which I cannot understand. The atom type OA is described in ffG45a3nb.itp as: ;name at.num mass charge ptype c6 c12 OA8 0.000 0.000 A 0.0022619536 1.505529e-06 and in ffG53a6nb.itp: OA8 0.000 0.000 A 0.0022619536 1.505529e-06 which are same parameters. However, according to Gromos developers the atom type OA has been changed between Gromos 45a3 and 53a6. The parameters given by Gromos developers for 45a3 are # IAC TYPESQRT(C6) SQRT(C12(1)) SQRT(C12(2)) SQRT(C12(3)) 3 OA 0.04756 1.1250E-3 1.227E-30.0 and for 53a6 3 OA 0.04756 1.100E-3 1.227E-3 0.0 The actual numbers are different for parameters used in Gromacs since the way to write parameters is different. My problem is that there is difference in OA type between 45a3 and 53a6 in parameters given by Gromos developers but not in the files distributed in Gromacs package. Can someone explain this? BR, Samuli Ollila -- gmx-users mailing listgmx-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
Re: [gmx-users] Gromos parameters for atom type OA
GROMOS force field builds the LJ parameters by multiplication of the square-rooted parameters per atom type (hence the SQRT(C6) and SQRT(C12) labels). In the case of the repulsion term (C12), up to three of such parameters are possible: SQRT(C12(1)) SQRT(C12(2)) SQRT(C12(3)), when combined with other atoms, depending on the desired repulsion strength (e.g. the enhanced C12(3) repulsion is used to keep charged groups separated). Which of the three is used depends on the combination of atoms, and is specified in an (asymmetric) matrix (see pages 14 and 15 in the pdf pages of 45a3 and 54a6 force fields from the GROMOS site, or in the ifp file the last lines for each atom type containing 1, 2 and 3). For the case of OA, this matrix specifies that the second C12 term is to be used when OA encountes another OA. So, according, to the ifp line you showed: C12(OA-OA) = SQRT(C12(2))_OA * SQRT(C12(2))_OA = 1.227E-3 * 1.227E-3 = 1.50553E-6 Which is the same for 45a3 and 54a6 force fields. Differences in the parameters will show up only in the cases where the SQRT(C12(1)) term for OA is to be used (e.g C12(OA-CH2)) Javier El 09/12/11 16:12, Samuli Ollila escribió: Dear all, I was comparing Gromos 45a3 and 53a6 force fields and I found something which I cannot understand. The atom type OA is described in ffG45a3nb.itp as: ;name at.num mass charge ptype c6 c12 OA8 0.000 0.000 A 0.0022619536 1.505529e-06 and in ffG53a6nb.itp: OA8 0.000 0.000 A 0.0022619536 1.505529e-06 which are same parameters. However, according to Gromos developers the atom type OA has been changed between Gromos 45a3 and 53a6. The parameters given by Gromos developers for 45a3 are # IAC TYPESQRT(C6) SQRT(C12(1)) SQRT(C12(2)) SQRT(C12(3)) 3 OA 0.04756 1.1250E-3 1.227E-30.0 and for 53a6 3 OA 0.04756 1.100E-3 1.227E-3 0.0 The actual numbers are different for parameters used in Gromacs since the way to write parameters is different. My problem is that there is difference in OA type between 45a3 and 53a6 in parameters given by Gromos developers but not in the files distributed in Gromacs package. Can someone explain this? BR, Samuli Ollila -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- gmx-users mailing listgmx-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
