Showing posts from July, 2015

Using gdb with gromacs

Download and compile gromacs 5.x cd gromacs; mkdir build ; cd build  cmake .. -DCMAKE_BUILD_TYPE=Debug Then, go to the methanol example cd share/gromacs/tutor/methanol/ grompp  Then enter gdb console and issue some commands $ gdb # that's where the gmx command lives exec ../../build/bin/gmx # read in the symbol table file ../../build/bin/gmx  # break on errors break _gmx_error # break on do_force function break do_force run mdrun -debug 1 -v -s This is not very practical - you can put the gdb commands into a file, gdb_cmds, and execute $ gdb -x gdb_cmds Note gdb has a ton of useful commands, google around References: - add pretty command to gdb - gdb tutorial handout