... 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.
