Dear Valentina, thanks for pointing it out. I tested the mapping and bonding stuff for quite a few things, never had an issue. My guess is that it is somehow connected with the mapping.
Could you please send me some example input where the problem occurs directly to rue...@votca.org. Thanks in advance, Victor 2011/10/2 Valentina <valentina_erast...@yahoo.co.uk>: >> 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. > > I will try. Thank you. > >> Sounds strange to me, but maybe Victor has an idea. Maybe you can >> provide us with a simple case that fails. > > I will put the details as soon as I get to the office (a bit later > today). > > Thank you very much, > V > > > On Oct 2, 1:28 pm, Christoph Junghans <jungh...@votca.org> wrote: >> 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. >> > >> >> > 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. >> > >> >> 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 >> > 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. > > -- You received this message because you are subscribed to the Google Groups "votca" group. 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