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] > <javascript:>> wrote: > >> >> >> On Thu, Jul 19, 2018 at 18:15 'Andrey Brukhno' via votca < >> [email protected] <javascript:>> 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] <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.
