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Bug #127

Segmentation fault in genion

Added by Erik Marklund almost 13 years ago. Updated over 12 years ago.

Status:
Closed
Priority:
High
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

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:

genion s $size/grompp_genion.tpr\
-o $size/genion.gro\
-np $NP\
-nn $NN\
-pq 1\
-nq -1\
-pname Na+\
-nname Cl
\
-random

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
Segmentation fault

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".

grompp_genion.tpr (1.52 MB) grompp_genion.tpr One of the many tpr files generating this error Erik Marklund, 01/26/2007 02:38 PM

History

#1 Updated by Erik Marklund almost 13 years ago

Created an attachment (id=104)
One of the many tpr files generating this error

#2 Updated by tiboli empty almost 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.

#3 Updated by David van der Spoel over 12 years ago

Fixed in CVS. An initialization was missing due to changes in data structures.

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