> 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 <[email protected]> wrote: > Am 2. Oktober 2011 12:02 schrieb Valentina <[email protected]>:> > 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 <[email protected]> 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 > >> <[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 > >> > 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 [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > 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 [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.
