Segmentation fault in genion
This error occurred when using the 3.3.99_development version. I am using the AMBER03 port to
simulate DNA. When adding 2 Na+ and 2 Cl+ to the system (already containing 14 Na+) genion stops
with a Segmentation Fault. The command given (from a csh script) was:
And the output:
Back Off! I just backed up genion1096565083.log to ./#genion1096565083.log.24#
WARNING: turning of free energy, will use lambda=0
Reading file XXL/grompp_genion.tpr, VERSION 3.3.99_development_20060330 (single precision)
Using a coulomb cut-off of 1 nm
Some really speedy debugging gave a hint that the error is related to the domain decomposition.
Oh, and "off" is misspelled in the warning "WARNING: turning of free energy, will use lambda=0".
#2 Updated by tiboli empty over 13 years ago
I ran into the same problem using the CVS version. My workaround was to use
3.3.1 to generate the box, solvate the protein, and add the ions. Once you have
a .gro file that contains your ions, then you can use the CVS version of grompp
to generate your .tpr file.