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.
