2013/6/27 <[email protected]>: > > > W dniu środa, 26 czerwca 2013 17:05:16 UTC+1 użytkownik Christoph Junghans > napisał: >> >> 2013/6/26 <[email protected]>: >> > Dear Gromacs Users, >> > >> > I want to run IBI to get nonbonded parameters with bonded tabulated >> > potentials (table_a0.xvg etc). How can I set up the command so Votca >> > will >> > mdrun gromacs with tables? >> Have look at the mdp file of the hexane example: >> >> <https://code.google.com/p/votca/source/browse/hexane/ibi/topol.top?repo=csg-tutorials> >> >> Block >> [ bonds ] >> ; ai aj funct c0 c1 c2 c3 >> 1 2 8 1 1.0 >> 2 3 8 1 1.0 >> 1st/2nd column atomnr. >> 3rd column = 8 = use tables >> 4th column = scale parameter for the table >> >> Christoph > > > Thank you... but I mean the command: mdrun -s topo.tpr -tablea table_a0.xvg > etc. > Do I have any influence on this command? The -tablea (actually, I guess, you mean -tableb) is only needed if you want to use file names different from gromacs default convention. Your example ( -tablea table_a0.xvg) would most likely make gromacs look to a table called table_a0_b0.xvg. (see mdrun -h)
As a side note, don't forget to add your tables to the filelist: <https://code.google.com/p/votca/source/browse/hexane/ibi/settings.xml?repo=csg-tutorials#102> If you really really want to change the option given to mdrun you can also do this inside <cg> <inverse> <gromacs> <mdrun> <opts>-tablea table_a0.xvg</opts> </mdrun> </gromacs> </inverse> </cg> But this is a "I hope you know what you are doing" option! Christoph > > Steven > >> >> >> > >> > Steven >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to [email protected]. >> > To post to this group, send email to [email protected]. >> > Visit this group at http://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/groups/opt_out. >> > >> > >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. > > -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
