Hi Sikandar, I have tried different ranges and different number of knots in the initial data for CG-CG param.init files, yet I am getting obvious discrepancies between the data provided and the data generated by csg_reupdate for CG-CG.pot.new at the veryy beginning of the RE iteration, i.e. at step_000.
Please check the new graph attached, exemplifying that the shifts along x-axis can be far from trivial (as opposed to what I thought before based on my first hands-on attempt). Clearly, the interpolated data (dashed lines) are not usable for a reliable RE iteration. I have 10 different potential types and all of them are skewed like that by csg_reupdate. I still hope that I am missing something which should be corrected in my input, and that it is not a typical interpolation behaviour with B-splines. Could you comment on this, please. Thanks Andrey On Monday, July 23, 2018 at 5:45:29 PM UTC+1, sikandar wrote: > > 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] > <javascript:>> wrote: > >> On Mon, Jul 23, 2018 at 9:28 AM, 'Andrey Brukhno' via votca >> <[email protected] <javascript:>> 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] <javascript:>. >> > To post to this group, send email to [email protected] >> <javascript:>. >> > 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] <javascript:>. >> To post to this group, send email to [email protected] <javascript:> >> . >> 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.
