[gmx-users] malloc error at mdrun step

Kalyan Reddy modugulas at gmail.com
Tue Dec 23 10:12:40 CET 2014

Dear Users,

I am learning free energy calculations using MD (Desolvation free energy of
Methane in water) from Justin Lemkul's tutorials. For this I have installed
gromacs-5.0.1 version on my Mac Pro workstation and proceeding with the
calculations as mentioned in the tutorials. When I ran mdrun step at
ENERGY MINIMIZATION 2: L-BFGS, I got stuck with the following error:

GROMACS:      gmx mdrun, VERSION 5.0.1
Executable:   /Volumes/DATA2/Kalyan/gromacs-5.0.1/gromacs/bin/gmx
Library dir:  /Volumes/DATA2/Kalyan/gromacs-5.0.1/gromacs/share/gromacs/top
Command line:
  mdrun -deffnm min0

Reading file min0.tpr, VERSION 5.0.1 (single precision)

The integration or electrostatics algorithm doesn't support parallel runs.
Using a single thread-MPI thread.

Using 1 MPI thread
mdrun(11149) malloc: *** error for object 0x1018a2408: incorrect checksum
for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
./job_0.sh: line 48: 11149 Abort trap

I am unable to figure out the source of the problem or the solution. Please
help me by providing solution to this problem.

Modugula E Kalyan Reddy
Ph No:  +91 - 9703825790

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