Hi Justin, So far I have been #including ffoplsaa.itp and running simulations. The reason I was after parameters is just to have a better indea on the FF parameters rather than just using them blindly, that's it :)
Thank you, On 31 July 2011 20:03, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Elisabeth wrote: > >> Thanks Justin for your guidance. By following your tips, I have now all >> the parameters I need... Please let me know if I am missing any [ angletypes >> ] or [ dihedraltypes ] for a hydrocarbon molecule. >> >> > Seems fine to me; grompp will complain if something is missing. Is there a > reason that you're trying to parse out certain parameters? It'd be far > easier to just #include "oplsaa.ff/forcefield.itp" in your topology and have > the entire OPLS-AA force field available to you, rather than reinventing the > wheel. > > -Justin > > Best, >> >> [ bondtypes ] >> ; i j func b0 kb >> CT CT 1 0.15290 224262.4 ; CHARMM 22 parameter file >> CT HC 1 0.10900 284512.0 ; CHARMM 22 parameter file >> >> [ angletypes ] >> ;i j k func th0 cth >> CT CT CT 1 112.700 488.273 ; CHARMM 22 parameter file >> CT CT HC 1 110.700 313.800 ; CHARMM 22 parameter file >> HC CT HC 1 107.800 276.144 ; CHARMM 22 parameter file >> >> [ dihedraltypes ] >> CT CT CT CT 3 2.92880 -1.46440 0.20920 -1.67360 >> 0.00000 0.00000 ; hydrocarbon all-atom >> CT CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 >> 0.00000 0.00000 ; hydrocarbon all-atom >> HC CT CT HC 3 0.62760 1.88280 0.00000 -2.51040 >> 0.00000 0.00000 ; hydrocarbon *new* 11/99 >> >> >> >> >> >> On 30 July 2011 07:40, Justin A. Lemkul <jalem...@vt.edu <mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Elisabeth wrote: >> >> Hello to all, >> >> I am looking for bonded and nonbonded parameters for C H atoms >> in saturated hydrocarbons. >> >> atom types are: >> Carbon atoms opls_135 opls_136 H opls_140 >> opls_135 12.01100 ; alkane CH3 >> opls_136 12.01100 ; alkane CH2 >> opls_140 1.00800 ; alkane H. >> >> Please help me out with the following: >> >> - I am wondering if I am selecting the correct values, for C-C >> and C-H bonds from ffoplsaabon.itp. >> >> >> The C-C bond is not correct for alkanes. It is for the C-C bond of >> oxalic acid, as the comment indicates. In ffnonbonded.itp, you can >> see how opls_* types are mapped to different bonded atom types (for >> instance, opls_135/136 are CT). Note that in the topology, you do >> not have to explicitly define values when using OPLS-AA; any bond >> between two defined bonded atom types will be automatically detected >> and used. >> >> >> C C 1 0.15100 292880.0 ; wlj oxalic acid, etc. >> HC C 1 0.10900 284512.0 ; wlj 7/96 >> >> - what does wlj mean? >> >> >> Probably someone's initials, which occur frequently to indicate >> either the source of the parameters or the individual that added >> them. In this case, my guess would be Jorgensen is the referenced >> individual here. >> >> - what are the units? >> >> >> This is in the manual. >> >> >> >> Angle >> >> CA CA CZ 1 120.000 585.760 ; wlj >> CA CA CR 1 120.000 527.184 ; >> CA CA CX 1 120.000 711.280 ; >> C CT Cl 1 109.800 577.392 ; wlj >> >> - I can not distinguish CA CZ .... What are they referring to? >> >> >> See the above tip about converting atom types in ffnonbonded.itp. >> >> >> [ dihedraltypes ] >> >> C C CT HC 3 0.17782 0.53346 0.00000 >> -0.71128 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000) >> >> - Is this what I need for oplsaa 135 136 140? >> >> >> Probably not. The comment indicates the dihedral is for >> dicarbonyls. The appropriate dihedral is: >> >> CT CT CT HC 3 0.62760 1.88280 0.00000 >> -2.51040 0.00000 0.00000 ; hydrocarbon all-atom >> >> Note how the comment indicates it is for use with hydrocarbons. >> Again, like bonds as described above, you do not need to explicitly >> list parameters in the topology. They will be inferred from the >> atom types. >> >> >> ffoplsaanb.itp. >> >> opls_135 CT 6 12.01100 -0.180 A >> 3.50000e-01 2.76144e-01 >> opls_136 CT 6 12.01100 -0.120 A >> 3.50000e-01 2.76144e-01 >> >> opls_140 HC 1 1.00800 0.060 A >> 2.50000e-01 1.25520e-01 >> >> - are these parameters for >> >> opls_135 12.01100 ; alkane CH3 >> opls_136 12.01100 ; alkane CH2 >> opls_140 1.00800 ; alkane H. >> >> ? >> >> >> Yes. >> >> >> Also in usr/local/gromacs/share/__**gromacs/top/ directory I can >> not find ffoplsaanb,itp and ffoplsaabon.itp for 4.5.4 whereas in >> previous versions these files were accessible. I am using itp >> files from version 4.0.7 and wanted to make sure the above >> parameters for oplsa_135 oplsa_136 and oplsa_140 have been >> remained unchanged in 4.5.4. Where can I find these files? >> >> >> The force field organization has changed, but the content of the >> force fields has not. This is described in the manual. All the >> equivalent files are now in the oplsaa.ff subdirectory. For >> backwards compatibility, the statement #include "ffoplsaa.itp" will >> indeed call the force field, because you will note that ffoplsaa.itp >> now simply calls the correct force field with #include >> "oplsaa.ff/forcefield.itp." >> >> -Justin >> >> -- ==============================**__========== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >> ==============================**__========== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >> Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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