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.
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.
