Hi Christoph & Sikandar, It's been a while since I asked the question below...
On Monday, July 23, 2018 at 7:51:14 PM UTC+1, Andrey Brukhno wrote: > > > >>> 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). > According to the equations each RE iteration should recalculate the averages corresponding to the "AA" (fine-detail) ensemble using a new CG representation (i.e. updated force-field), and this is what I fail to find in the tutorial for spce/re. Could you please clarify this. Andrey > > >> >> > 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.
