grompp floating point exception with Andersen thermostat
I get a "Floating point exception (core dumped)" message from gmx grompp (version 2016.3) with the following files. The error could be reproduced on a different computer.
This might be related to the Anderson thermostat but I'm not sure. Interestingly i could grompp and mdrun the simulation with a gromacs 4.6.7 installation.
The full output of
gmx grompp -debug is:
Will write debug log file: gmx.debug NOTE 1 [file grompp.mdp, line 28]: grompp.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# Setting the LD random seed to -602093053 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'CHA' Setting gen_seed to 216421358 Velocities were taken from a Maxwell distribution at 300 K Removing all charge groups because cutoff-scheme=Verlet checking 91 functypes Analysing residue names: There are: 2 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... NOTE 2 [file grompp.mdp]: Andersen temperature control methods assume nsttcouple = 1; there is no need for larger nsttcouple > 1, since no global parameters are computed. nsttcouple has been reset to 1 Number of degrees of freedom in T-Coupling group System is 30.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 2.000 nm, buffer size 0.000 nm Set rlist, assuming 4x4 atom pair-list, to 2.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Floating point exception (core dumped)
Fix grompp with Andersen massive and no COM removal
Fixed a floating point exception leading to a segv.
Also fixed possible different rounding for the interval for
Andersen massive in grompp in mdrun for the common case where tau_t
is a multiple of delta_t.
#1 Updated by Berk Hess about 2 years ago
- Subject changed from grompp floating point exception to grompp floating point exception with Andersen thermostat
- Status changed from New to In Progress
- Assignee set to Berk Hess
- Target version set to 2016.5
- Affected version - extra info set to likely any verion with Andersen massive
The issue is triggered because you are using the combination of Andersen massive with no center of mass motion removal. You can avoid it by turning on center of mass motion removal.
If will push up a fix to gerrit.