What does “Fatal error: Routine gmx_tx called in libnet.c” mean?
You probably made a parallel mdrun without typing make distclean. The error messages tells you that the GROMACS library you are using doesn’t support parallel runs. • My simulation seems to be running, but shouldn’t there be any output? • Your simulation might simply be (very) slow, and since output is buffered, it can take quite some time for output to appear in the respective files. If you are trying to fix some problems and you want to get output as fast as possible, you can set the environment variable LOG_BUFS to 0 by using setenv LOG_BUFS 0, this disables output buffering. Use unsetenv LOG_BUFS to turn buffering on again. • Something might be going wrong in your simulation, causing e.g. not-a-numbers (NAN) to be generated (these are the result of e.g. division by zero). Subsequent calculations with NAN’s will generate floating point exceptions which slow everything down by orders of magnitude. On a SGI system this will usually result in a large percentage of CPU time being devote
