GROMACS version: 2018.1
GROMACS modification: No
I’m a postdoc mentoring an undergrad in MD simulations using Gromacs. He is using Gromacs 2018.1 (admittedly quite old) because that’s what is available on the node assigned to him.
The undergrad has a 100 ps trajectory, traj.trr, with 1001 frames, each separated by 0.1 ps. I verified this by running ‘gmx check -f traj.trr’. (His simulation was 100,000 steps, with a timestep of 0.001 ps and with configurations saved every 100 steps.)
I asked him to use ‘gmx trjconv -f traj.trr -dt 1 -o newtraj.trr’ to save frames only every 1 ps from traj.trr to newtraj.trr. The student and I both receive this error message from Gromacs 2018.1:
munmap_chunk(): invalid pointer Aborted (core dumped)
However, newtraj.trr is created, and when I run ‘gmx check’ on it, it looks fine:
Item #frames Timestep (ps) Step 101 1 Time 101 1 Lambda 101 1 Coords 101 1 Velocities 2 100 Forces 0 Box 101 1
newtraj.trr also looks fine when visualized in VMD.
Does anyone have any idea of why we’re getting the error “munmap_chunk(): invalid pointer; Aborted (core dumped)”? Does this necessarily suggest the trajectory is corrupted in some way, even if my tests on it so far appear fine? Or could this suggest that Gromacs was compiled incorrectly on that node?
I transferred the trajectory to another node running the same version of Gromacs. I get the same error message when I run trjconv on it. (This does not, however, I think rule out a compilation problem because the system administrator may have done some sort of batch compilation.)
Carnegie Mellon University