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.
