Am 2. Oktober 2011 12:02 schrieb Valentina <valentina_erast...@yahoo.co.uk>: > A, that makes sense. I have done simple inversion, but its looking > like i may need a few iterations still. It could be possible that the code in the bonded branch already works if one provides a reasonable potential input ($name.pot.in) and ensures the refinement region (min to max) is always well sampled.
> Also, btw, though I should tell you. I have noticed a bit of a problem > with bonded potentials produced by csg_botzmann. I have a simple > molecule that is put into End-Ceter-Center-End bids. I have used > csg_boltzmann to do inversion and also did it by hand myself to > compare. Center-Center bonds are perfect, but End-Center ones are not > right. I haven't yet figured out why. Sounds strange to me, but maybe Victor has an idea. Maybe you can provide us with a simple case that fails. Cheers, Christoph > > V > > > On Oct 2, 8:07 am, Christoph Junghans <jungh...@votca.org> wrote: >> 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 <valentina_erast...@yahoo.co.uk>: >> >> >> >> >> >> >> >> >> >> > 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 <valentina_erast...@yahoo.co.uk> 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 votca@googlegroups.com. >> > To unsubscribe from this group, send email to >> > votca+unsubscr...@googlegroups.com. >> > For more options, visit this group >> > athttp://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 votca@googlegroups.com. > To unsubscribe from this group, send email to > votca+unsubscr...@googlegroups.com. > 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 votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
