[gmx-users] atomtypes, parameters in file do not match parameters in manual
Hello all. I'm new to Gromacs, so sorry for this (probably naive) question: In Table 5.3 in the Gromacs manual version 3.3, the parameters for [atomtypes] are: atom type, mass, charge, particle type, V and W. In the Gromacs directory containing the the force fields (/usr/local/gromacs/share/gromacs/top on my machine) the ffoplsaanb.itp file begins with the following lines: [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_001 C 6 12.01100 0.500 A3.75000e-01 4.39320e-01 ; SIG Why do the manual parameters not match the parameters in the file? Which of the two are correct? Kind regards Andreas ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] atomtypes, parameters in file do not match parameters in manual
Andreas Kring wrote: Hello all. I'm new to Gromacs, so sorry for this (probably naive) question: In Table 5.3 in the Gromacs manual version 3.3, the parameters for [atomtypes] are: atom type, mass, charge, particle type, V and W. In the Gromacs directory containing the the force fields (/usr/local/gromacs/share/gromacs/top on my machine) the ffoplsaanb.itp file begins with the following lines: [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_001 C 6 12.01100 0.500 A3.75000e-01 4.39320e-01 ; SIG Why do the manual parameters not match the parameters in the file? Hm Iäm sure you know the answer to that one. Which of the two are correct? The files. Kind regards Andreas ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] atomtypes, parameters in file do not match parameters in manual
Andreas Kring wrote: Hello all. I'm new to Gromacs, so sorry for this (probably naive) question: In Table 5.3 in the Gromacs manual version 3.3, the parameters for [atomtypes] are: atom type, mass, charge, particle type, V and W. In the Gromacs directory containing the the force fields (/usr/local/gromacs/share/gromacs/top on my machine) the ffoplsaanb.itp file begins with the following lines: [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_001 C 6 12.01100 0.500 A3.75000e-01 4.39320e-01 ; SIG Why do the manual parameters not match the parameters in the file? Which of the two are correct? There's an undocumented feature where the fields in an [ atomtypes ] line follow one of several possible formats and grompp is smart about working one which field means what. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
