On Wed, Aug 5, 2020 at 9:04 PM Pragati Sharma <[email protected]> wrote: > > > It is the mdrun command, where the error comes. I have attached the > inverse.log file here also. Thanks. That usually means your system exploded, maybe there is a message from mdrun in one of the log files as well. The reason for that is most likely that one of the bonded interactions is screwed up. You could try to run it with harmonic interactions as a start to check that.
Christoph > > > > > On Wednesday, 5 August 2020 17:15:42 UTC+5:30, Pragati Sharma wrote: >> >> Dear all, >> >> I am trying to run CG simulations of 5mer-polybutadiene using IBI method and >> following hexane tutorial. >> I am getting segmentation fault at step 1, when I run csg_inverse command. >> Below are the steps I followed and files attached. Please guide me towards >> the probable reason of the error. >> >> 1. csg_mapp and csg_gmxtopol " generate cg.gro and cg.top >> >> 2.Run run_Boltzman.sh script to get target distributions and potentials >> (This gives tabulated potential files for bonded interactions only) >> >> 3. Run run.sh script (for getting non-bonded potentials): I provide the >> tabulated bonded potentials obtained in step 2 here for simulation and run >> csg_inverse. In this step the error comes. >> >> Sometimes the error shows infinite potential energy in the system. >> >> I guess there is some issue with my bonded potentials. I have read you have >> to "manually delete poorly sampled parts" from potential files. How to do >> it, If that is the reason. >> >> I am attaching the potential files here. >> >> Thanks >> >> >> >> >> > -- > 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/3a89f8a1-74ba-4942-9581-5bb248b77ceco%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/CAHG27e7P4MsEtBBcj2iRiUQOLSwBEbyOVShSt65uxfu1gNEZuQ%40mail.gmail.com.
