free energy code introduces a crash in recent GROMACS versions for a system which is stable under older gromacs versions and with free energy off
In the process of trying to test some new features in version 5.0, I resurrected an old test system which I used extensively under GROMACS 3.3.4 and prior. This test system still runs under GROMACS 4.6.3 and the 5.0 pre-release I'm working with, but ONLY if the free energy code is turned off. If I turn free energy on, I get a constraints warning of a deviation of 'nan' as sooon as I start running dynamics (though minimization works fine) and the simulation hangs. It will run forever, it appears, so I end up actually having to manually kill it (and in fact ctrl-C and ctrl-D don't kill it -- I actually have to use 'kill -9 (pid)').
I am attaching a test system to reproduce the problem. As currently set up, it will run properly under 4.6.3 (and I believe 4.6.5) and the 5.0 pre-release I'm working with, but change free_energy to 'yes' in the mdp files, or the mdp file for equil_nvt, and it will hang.
I have verified that this system still works properly with the free energy code turned on under older GROMACS versions (3.3.4).
Please note that this appears particularly important and problematic, since a system run at lambda=0 with the free energy turned ON should be identical to a system run with the free energy code turned off. That's how I have this set up, so it seems particularly concerning that it hangs with free energy turned on, but not with it off.
#2 Updated by David Mobley about 3 years ago
OK, so it looks like the issue is really two things, one of which is my fault:
1) In resurrecting my test system, I had to set up the perturbation again, and I forgot to fill in the B state mass column in the atomtypes section, resulting in some B state masses which are zero, as you note
2) There is apparently a difference in how missing B state masses are handled in 4.x and later as compared to 3.x, in that I can run this system at lambda = 0 even with zero B state masses in older GROMACS versions, but not under the new ones. Presumably when the lambda vector stuff was implemented for 4.6 this changed.
In any case, presumably this is not exactly a bug, then, but also it would be nice to avoid silent failure. Maybe a specific warning any time any of the atoms in a system has a zero mass in either A or B state?
#5 Updated by Erik Lindahl almost 3 years ago
- Tracker changed from Bug to Feature
- Status changed from Accepted to Resolved
- Target version changed from 4.6.x to 5.0
As Berk wrote, this is not a bug, but incorrect topology. However, I added a check for stateB to the place where we already check masses for stateA in grompp - that should help catch things like this automatically next time.