Hi Andrey, Could you please send me the raw data of your plots?
Thanks, Sikandar On Tue, Nov 13, 2018 at 4:32 PM 'Andrey Brukhno' via votca < [email protected]> wrote: > 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]> >> 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. > 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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