W dniu czwartek, 27 czerwca 2013 16:56:37 UTC+1 użytkownik Christoph Junghans napisał: > > 2013/6/27 <[email protected] <javascript:>>: > > > > > > 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 >
Thank you Christoph! Steven > > > > > > 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] <javascript:>. > > To post to this group, send email to [email protected]<javascript:>. > > > 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.
