On Mon, Jul 23, 2018 at 5:07 PM, Christoph Junghans <[email protected]> wrote:
> On Mon, Jul 23, 2018 at 9:22 AM, 'Andrey Brukhno' via votca > <[email protected]> wrote: > > > > > > On Friday, July 20, 2018 at 2:08:19 AM UTC+1, Christoph Junghans wrote: > >> > >> > >> > >> On Thu, Jul 19, 2018 at 17:26 'Andrey Brukhno' via votca > >> <[email protected]> wrote: > >>> > >>> > >>> > >>> On Thursday, July 19, 2018 at 7:57:57 PM UTC+1, Christoph Junghans > wrote: > >>>> > >>>> On Thu, Jul 19, 2018 at 10:44 AM, 'Andrey Brukhno' via votca > >>>> <[email protected]> wrote: > >>>> > I get: > >>>> > > >>>> > ... <normal output> ... > >>>> > Total number of parameters to optimize: 333 > >>>> > an error occurred: > >>>> > property not found: scale > >>>> See here: > >>>> > >>>> https://github.com/votca/csg-tutorials/blob/master/spce/re/ > settings.xml#L69 > >>>> > >>>> Christoph > >>>> > >>> > >>> Actually, I am a bit confused not seeing re.traj tag for atomistic > >>> trajectory. I thought RE iteration requires recalculating CG averages > in > >>> over atomistic ensemble (trajectory) for every new set of CG > potentials? > >>> > >>> Also, what about the corresponding re.topology tag - specifying what? > >> > >> Both options exist: > >> > >> https://github.com/votca/csg/blob/master/share/scripts/ > inverse/update_re.sh#L30 > >> > > > > Just to clarify: above you confirm that the two tags > > `cg.inverse.$sim_prog.re.topol' and `cg.inverse.$sim_prog.re.traj' > specify > > the tpr and xtc/trr files for the original fine-detail (atomistic) > > simulation? > No these are just options, which allow you to overwrite the > coarse-grained topology and trajectory. > Nothing atomistic here! > If so, I am back to my question of how are the averages over fine detail (atomistic) ensemble calculated for a new CG model/FF at each iteration? I am referring to Eqs. 2.24 and 2.26 in the manual (page 8). > > > For reference, below is the extract from `share/votca/xml/csg_defaults. > xml', > > where no traj tag is present (this is for v1.4.1, so perhaps in v1.5.1 > the > > tag is there?): > > > > <re> > > <topol> > > <DESC>Special topology file to be used for > > csg_reupdate</DESC> > > </topol> > > </re> > > > > Btw, my original question was: why these are not specified in > `settings.xml' > > in the (spce/re) case you referred to above? > If they are not specified the default topology (topol.tpr) and default > trajectory (traj.xtc) are used. > > > > > Thanks / Andrey > > > >> Christoph > >> > >>> > >>> Andrey > >>> > >>>> > >>>> > >>> -- > >>> 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 https://groups.google.com/group/votca. > >>> For more options, visit https://groups.google.com/d/optout. > >> > >> -- > >> 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 https://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de > > -- > You received this message because you are subscribed to a topic in the > Google Groups "votca" group. > To unsubscribe from this topic, visit https://groups.google.com/d/ > topic/votca/2Otu4QhLG_A/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > -- 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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
