To make it short, IBI for bonded interactions is not implemented yet. It has been on the todo list for a year (issue 11 - <https://code.google.com/p/votca/issues/detail?id=11>) I have started working on this a while ago in the 'bonded' branch of csg, but it is far from being finished.
However for most systems simple Boltzmann inversion (BI) is enough as bonded interactions are much stiffer. Cheers, Christoph Am 2. Oktober 2011 00:27 schrieb Valentina <[email protected]>: > Also, have a error: > # Result of 'csg_property --file /home/d47fvj/C12-BND/settings-BND.xml > --path cg.non-bonded.name --short --print .' was empty # > > Do I have to have cg.non-bonded. section in any case? > > Thank you, > V > > On Oct 1, 11:15 pm, Valentina <[email protected]> wrote: >> Hello, >> >> I am a bit stuck here. >> >> If I want to do IBI for bonded interactions, I will create a CG >> starting .gro and .top >> for .top I would need to feed in a tabulated potential (created by >> initial inversion of distibutions) in the form of table_b1.xvg >> >> so in the settings.xml I provide a target potential bonds-EC.tgt >> <bonded> >> <name>E-C</name> >> <min>0</min> >> <max>1.50</max> >> <step>0.01</step> >> <inverse> >> <target>bonds-EC.tgt</target> >> <do_potential>1 0 0</do_potential> >> <post_update>scale</post_update> >> <post_update_options> >> <scale>1</scale> >> </post_update_options> >> <gromacs> >> <table>table_b1.xvg</table> >> </gromacs> >> </inverse> >> </bonded> >> >> also I have files to be transferred, where I have table_b1.xvg being >> carried through to every new step >> <filelist>grompp.mdp topol.top table.xvg table_a1.xvg table_b1.xvg >> table_b2.xvg index.ndx</filelist> >> >> So this is where I am confused, how do I make it to update >> table_b1.xvg after every step? >> >> Many thanks, >> V > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > > -- Christoph Junghans Votca Core Developer Web: http://www.votca.org -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
