[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

[Andrew Bostick]

Dear gromacs users

I am doing md simulation on the a protein with 190 residues.

I did minimization and equilibration without problem and error.

But in production run step (last md simulation with 15000000 steps),
in step 6500000, I encountered with following error:

File input/output error:
Cannot write trajectory frame; maybe you are out of disk space.

my mdp file is as follows:
-----------------------------------------------------------------------------------------
title        = opls Protein MD
; Run parameters
integrator    = md                    ; leap-frog integrator
nsteps        = 15000000                ; 0.002 * 500000 = 1000 ps, 30 ns
dt             = 0.002                    ; 2 fs
; Output control
nstxout        = 3000                     ; save coordinates every 2 ps
nstvout        = 3000                     ; save velocities every 2 ps
nstxtcout    = 3000                     ; xtc compressed trajectory output
every 2 ps
nstenergy    = 3000                     ; save energies every 2 ps
nstlog        = 3000                     ; update log file every 2 ps
energygrps  = Protein Ion
; 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
ns_type        = grid                    ; search neighboring grid cells
nstlist        = 5                        ; 10 fs
rlist        = 1.0                     ; short-range neighborlist cutoff
(in nm)
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    = 4                        ; cubic interpolation
fourierspacing    = 0.16                ; grid spacing for FFT
; Temperature coupling is on
tcoupl        = V-rescale                ; modified Berendsen thermostat
tc-grps        = Protein Non-Protein    ; two coupling groups - more
accurate
tau_t        = 0.1    0.1                ; time constant, in ps
ref_t        = 300     300                ; 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                    ; Velocity generation is off
-----------------------------------------------------------------------------------------

If I use df -h command to know disk space, I obtained following information:

Filesystem      Size  Used Avail Use% Mounted on
/dev/sda3       220G   14G  196G   7% /
none            4.0K     0  4.0K   0% /sys/fs/cgroup
udev            3.0G  4.0K  3.0G   1% /dev
tmpfs           607M  1.3M  606M   1% /run
none            5.0M     0  5.0M   0% /run/lock
none            3.0G  152K  3.0G   1% /run/shm
none            100M   64K  100M   1% /run/user
/dev/sda6       245G   61G  184G  25% /media/pdfco/my dear
/dev/sda2       220G   85G  136G  39% /media/pdfco/Windows
/dev/sda5       245G   43G  202G  18% /media/pdfco/nazif
------------------------------------------------------------------------------------------

Is my computer system suitable for this md simulation?

How to solve this error?

Any help will highly appreciated.