Hi Andrey, In the case of non-bonded CG pair potentials, the AA ensemble average values for dU/d\lambda and d^2U/d\lambda^2 are computed using the reference AA pair correlations (i.e., CG-CG.dist.tgt). See Eq. 2.11 in http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131754
-- Sikandar On Wed, Aug 1, 2018 at 5:21 AM 'Andrey Brukhno' via votca < [email protected]> wrote: > 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. > -- 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.
