On Mon, Apr 5, 2021 at 2:20 PM Satyen Dhamankar <[email protected]> wrote: > > Hello, > > I am performing a coarse-grained simulation of benzene, where I am converting > C6H6 into two beads. Where each bead is essentially C3H3, and they are > connected by a bond. > > I want to perform IBI on this coarse-grained simulation using votca and gmx, > but I am having some problems. > > The command I am running is: > csg_inverse --options settings.xml > > I am getting an energy divergence (blows up to infinity) when votca runs > mdrun. This is the error I see in my inverse.log file: > > Program: gmx mdrun, version 2019.6 > Source file: src/gromacs/mdlib/sim_util.cpp (line 752) > MPI rank: 1 (out of 6) > Fatal error: > Step 0: The total potential energy is inf, which is not finite. The LJ and > electrostatic contributions to the energy are inf and 0, respectively. A > non-finite potential energy can be caused by overlapping interactions in > bonded interactions or very large or Nan coordinate values. Usually this is > caused by a badly- or non-equilibrated initial configuration, incorrect > interactions or parameters in the topology. > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > I am running a minimization script, but I don't see why energy is blowing up. > > I also am unsure of what the table_b1.xvg and table_a1.xvg files are for. I > naively got these files from the hexane tutorial. What are these files for? > How do I make them? These two tables are for the bonded interactions, they are just boltzmann-inverted tables from the bonded distributions (do that by hand or use csg_boltzmann). You could also use harmonic potentials as a start to make your life easier.
Christoph > > I have attached my grommp.mdp, conf.gro, settings.xml, topol.top and tables > files. > > Any advice you have would be appreciated! > > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/956dbed6-f6a1-4269-866c-a4a8c5a6428cn%40googlegroups.com. -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- 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 view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e6TmLO8_ie2cqetgMNY-EhEaLot-ta005%2BEVpbvrLBhVA%40mail.gmail.com.
