[gmx-users] gmx: malloc(): memory corruption

[Quyen V. Vu]

Dear GMX user,
I have just installed *gromacs 2016.1* on my machine and run mdrun with
these option:
-------------------------------------------------------------------------------------------------
title                   = 50AT DNA MD simulation
; Run parameters
integrator              = md                    ; leap-frog integrator
nsteps                  = 5000                  ; 2 * 5000000 = 10000 ps
(10 ns)
dt                      = 0.002                 ; 2 fs
; Output control
nstxout                 = 500                   ; save coordinates every
20.0 ps
nstvout                 = 500                   ; save velocities every
20.0 ps
nstenergy               = 500                   ; save energies every 20.0
ps
nstlog                  = 500                   ; update log file every
20.0 ps
nstxout-compressed      = 500                   ; save compressed
coordinates every 20.0 ps
; nstxout-compressed replaces nstxtcout
compressed-x-grps       = SYSTEM                ; replaces xtc-grps
; Bond parameters
continuation            = yes                   ; Restarting after NPT
constraint_algorithm    = lincs                 ; holonomic constraints
constraints             = all-bonds             ; all bonds (even heavy
atom-H bonds) constrained
lincs_iter              = 1                     ; accuracy of LINCS
lincs_order             = 4                     ; also related to accuracy
; Neighborsearching
cutoff-scheme           = Verlet
ns_type                 = grid                  ; search neighboring grid
cells
nstlist                 = 40                    ; 20 fs, largerly
irrelevant with Verlet scheme
rcoulomb                = 1.0                   ; short-range electrostatic
cutoff (in nm)
rvdw                    = 1.0                   ; short-range van der Waals
cutoff (in nm)
; Electrostatics
coulombtype             = PME                   ; Particle Mesh Ewald for
long-range electrostatics
pme_order               =5                      ; cubic interpolation
fourierspacing          = 0.16                  ; grid spacing for FFT
; Temperature coupling is on
tcoupl                  = Nose-Hoover           ; More accurate thermostat
nsttcouple              = 1
tc-grps                 = DNA SOL ION           ; three coupling groups -
more accurate
tau_t                   = 0.1 0.1 0.1           ; time constant, in ps
ref_t                   = 298 298 298           ; reference temperature,
one for each group, in K
; Pressure coupling is on
pcoupl                  = Parrinello-Rahman     ; Pressure coupling on in
NPT
pcoupltype              = isotropic             ; uniform scaling of box
vectors
tau_p                   = 2.0                   ; time constant, in ps
ref_p                   = 1.0                   ; reference pressure, in bar
compressibility         = 4.5e-5                ; isothermal
compressibility of water, bar^-1
; Periodic boundary conditions
pbc                     = xyz                   ; 3-D PBC
; Dispersion correction
DispCorr                = EnerPres              ; account for cut-off vdW
scheme
; Velocity generation
gen_vel                 = no                    ;do not generate Velocity
-------------------------------------------------------------------------------------------------
*After that, I use trjconv to get position of DNA by command:*
       gmx trjconv -s md.tpr -f md.xtc -o md_mol.xtc -pbc mol -ur compact
and gmx prompt:
Group     0 (         System) has 500179 elements
Group     1 (            DNA) has  3198 elements
Group     2 (             NA) has   129 elements
Group     3 (             CL) has    31 elements
Group     4 (          Water) has 496821 elements
Group     5 (            SOL) has 496821 elements
Group     6 (      non-Water) has  3358 elements
Group     7 (            Ion) has   160 elements
Group     8 (             NA) has   129 elements
Group     9 (             CL) has    31 elements
Group    10 ( Water_and_ions) has 496981 elements

*I type 1 and press Enter then get message:*
Select a group: 1
Selected 1: 'DNA'
Reading frame       0 time    0.000
Precision of md.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)

Back Off! I just backed up md_mol.xtc to ./#md_mol.xtc.2#
*** Error in `gmx': malloc(): memory corruption: 0x0000000001be5c30 ***
Aborted


*Could you tell me this error is caused by me or gromacs program?*
*Thank you*