Hi Andrey, What do the lines in your plot correspond to? Are you plotting param.init vs the potential computed from them? If so, the knot values in parameter file and the potential are not the same. Please see Eq. 3.1 from http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131754 .
Let me know if I missed anything. -- Sikandar On Mon, Jul 23, 2018 at 9:11 AM Christoph Junghans <[email protected]> wrote: > On Mon, Jul 23, 2018 at 9:28 AM, 'Andrey Brukhno' via votca > <[email protected]> wrote: > > Any comment on this "shift" issue? > > I tried to find the relevant script in share/votca/scripts/inverse but it > > seems that all interpolation is done by `csg_reupdate' app, and I didn't > > have time up to now to look into the code. > No idea, that is more a question for Sikandar! > > > > > Thanks! / Andrey > > > > On Friday, July 20, 2018 at 11:59:37 AM UTC+1, Andrey Brukhno wrote: > >> > >> ... > >> As a matter of fact, the problem appears to be not a poor interpolation > >> but a systematic shift in the X axis (by the size of the grid bin in the > >> original data, i. e. param.init files) - see the corrected graph where I > >> simply shifted all the interpolation curves by dx=0.02. > >> > >> So I conclude that something is fishy about the x column in the pot.cur > >> files. > >> > >> Andrey > >> > >> On Friday, July 20, 2018 at 11:45:27 AM UTC+1, Andrey Brukhno wrote: > >>> > >>> Hi Christoph & Sikandar, > >>> > >>> Thank you both for your replies! > >>> > >>> Per your suggestions, I have compared the potentials generated (i.e. > >>> B-spline interpolated) based on the initial guesses provided as > >>> CGi-CGj.param.init files with the original data (i.e. the contents of > those > >>> param.init files). I found systematic discrepancies (see the attached > graph, > >>> where only 3 potentials shown)! - No wonder I am getting into trouble > after > >>> a new simulation with the potentials being that much off, especially at > >>> shorter distances. > >>> > >>> Is it normal to have such large differences with the interpolated data? > >>> I would think that there must be a way to improve on the interpolation > by > >>> varying something in the input - ? > >>> Is it where the LJ repulsive core would help? (Although I think that > >>> would be an ad hoc workaround for the poor interpolation issue.) > >>> > >>> It seems I still need your advice here, based on your practical > >>> experience. > >>> > >>> Andrey > >>> > >>> On Friday, July 20, 2018 at 7:39:45 AM UTC+1, sikandar wrote: > >>>> > >>>> Hi Andrey, > >>>> > >>>> Below are some of the things you can try to address this issue. > >>>> > >>>> 1. Make sure the potentials generated from your initial parameters are > >>>> physically consistent > >>>> 2. Increase number of timesteps in CG simulation > >>>> 3. Decrease the scaling parameter > >>>> 4. If your CG system has charges, then you may need to add a LJ type > >>>> potential to your CBSPL CG potential after every CG update to ensure > that > >>>> the CG potential is repulsive enough at short distances and does not > allow > >>>> overlap of oppositely charged sites. You can enable this option by > >>>> specifying post_update block for every CG potential pair as > >>>> <non-bonded> > >>>> ... > >>>> <post_update>lj</post_update> > >>>> <post_update_options> > >>>> <lj> > >>>> <c6> LJ C6 Value </c6> > >>>> <c12> LJ C12 Value </c12> > >>>> </lj> > >>>> </post_update_options> > >>>> ... > >>>> </non-bonded> > >>>> > >>>> I hope this helps. > >>>> > >>>> Best, > >>>> Sikandar > >>>> > >>>> On Thu, Jul 19, 2018 at 6:13 PM Christoph Junghans <[email protected] > > > >>>> wrote: > >>>>> > >>>>> > >>>>> > >>>>> On Thu, Jul 19, 2018 at 18:15 'Andrey Brukhno' via votca > >>>>> <[email protected]> wrote: > >>>>>> > >>>>>> Hello, > >>>>>> > >>>>>> I managed to run the RE iteration for a system with 10 non-bonded > >>>>>> potentials (types).. well, the first iteration anyway, where it > terminated > >>>>>> after about an hour of running csg_reupdate with the following > error: > >>>>>> > >>>>>> Hessian NOT a positive definite! > >>>>>> This can be a result of poor initial guess or ill-suited CG > potential > >>>>>> settings or poor CG sampling. > >>>>>> > >>>>>> My understanding is, sometimes this might happen, but this was my > >>>>>> second trial where I virtually doubled (44 -> 88) the number of > knots and > >>>>>> (in both cases) I use potentials derived from an earlier IBI > iteration. > >>>>>> > >>>>>> I would really appreciate clues, hints or general advice as to how > to > >>>>>> alleviate the issue. > >>>>> > >>>>> Sikandar will know more, but most likely you will need to throw away > >>>>> some frames at the beginning of the trajectory and run the > iterations for a > >>>>> bit longer! > >>>>> > >>>>> Christoph > >>>>>> > >>>>>> > >>>>>> Thanks! > >>>>>> 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. > > > > -- > > 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. > -- You received this message because you are subscribed to the Google Groups "votca" group. 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