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grompp floating point exception with Andersen thermostat - Redmine #2256

Archive from user: Marvin Bernhardt

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 grompmdp, line 28]:
  grompmdp 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.md3#
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 grompmdp]:
  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)

(from redmine: issue id 2256, created on 2017-09-22 by gmxdefault, closed on 2017-12-11)

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.

Fixes #2256

Change-Id: I161e8a9db2c31fde8a6e8c2fd32551b21423fd9b