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

[Andrew Bostick]

Dear Mark

I'm apologize.  You are right. I should give more indication and
information you to help me.

I used chmod -R 777 directory containing pdb and mdp files. Then I did MD
simulation again:

(pdb2gmx ...> editconf ........> em ...> npt eq ...> md)

My problem is in md step (md.trr file).

1) After using ls -l:

-rw-r--r-- 1 pdfco pdfco 137377  April 22 09:37 box.gro
-rw-r--r-- 1 pdfco pdfco 137377  April 22 09:37 conf.gro
-rw-r--r-- 1 pdfco pdfco 139904  April 22 09:44 em.edr
-rw-r--r-- 1 pdfco pdfco 1814139 April 22 09:44 em.gro
-rw-r--r-- 1 pdfco pdfco 353777  April 22 09:44 em.log
-rwxrwxrwx 1 pdfco pdfco 958     April 9 2012 em.mdp
-rw-r--r-- 1 pdfco pdfco 1673608 April 22 09:43 em.tpr
-rw-r--r-- 1 pdfco pdfco 483876  April 22 09:44 em.trr
-rwxrwxrwx 1 pdfco pdfco 171111  April 16 16:20 hgh.pdb
-rwxrwxrwx 1 pdfco pdfco 960     April 9 2012 ions.mdp
-rw-r--r-- 1 pdfco pdfco 1672380 April 22 09:38 ions.tpr
-rw-r--r-- 1 pdfco pdfco 972688  April 24 05:56 md.cpt
-rw-r--r-- 1 pdfco pdfco 2105052 April 24 06:06 md.edr
-rw-r--r-- 1 pdfco pdfco 4723361 April 24 06:07 md.job
-rw-r--r-- 1 pdfco pdfco 1498538 April 24 06:07 md.log
-rwxrwxrwx 1 pdfco pdfco 2251    April 14 10:18 md.mdp
-rw-r--r-- 1 pdfco pdfco 11314   April 22 18:10 mdout.mdp
-rw-r--r-- 1 pdfco pdfco 972688  April 24 05:56 md_prev.cpt
-rw-r--r-- 1 pdfco pdfco 1995920 April 22 18:11 md.tpr
-rw-r--r-- 1 pdfco pdfco 2147483647 April 24 06:07 md.trr   **************
-rw-r--r-- 1 pdfco pdfco 322065544  April 24 06:06 md.xtc
-rw-r--r-- 1 pdfco pdfco 972048  April 22 17:10 npt.cpt
-rw-r--r-- 1 pdfco pdfco 337488  April 22 17:10 npt.edr
-rw-r--r-- 1 pdfco pdfco 2781651 April 22 17:10 npt.gro
-rw-r--r-- 1 pdfco pdfco 356914  April 22 17:10 npt.job
-rw-r--r-- 1 pdfco pdfco 369014  April 22 17:10 npt.log
-rwxrwxrwx 1 pdfco pdfco 2317    April 14 09:40 npt.mdp
-rw-r--r-- 1 pdfco pdfco 972048  April 22 17:10 npt_prev.cpt
-rw-r--r-- 1 pdfco pdfco 1963760 April 22 14:25 npt.tpr
-rw-r--r-- 1 pdfco pdfco 484783632  April 22 17:10 npt.trr
-rw-r--r-- 1 pdfco pdfco 72710736   April 22 18:08 npt.xtc
-rw-r--r-- 1 pdfco pdfco 971700  April 22 12:26 nvt.cpt
-rw-r--r-- 1 pdfco pdfco 283252  April 22 12:26 nvt.edr
-rw-r--r-- 1 pdfco pdfco 2781651 April 22 12:26 nvt.gro
-rw-r--r-- 1 pdfco pdfco 356883  April 22 12:26 nvt.job
-rw-r--r-- 1 pdfco pdfco 383651  April 22 12:26 nvt.log
-rwxrwxrwx 1 pdfco pdfco 2095    April 14 09:40 nvt.mdp
-rw-r--r-- 1 pdfco pdfco 971700  April 22 12:26 nvt_prev.cpt
-rw-r--r-- 1 pdfco pdfco 1963760 April 22 09:45 nvt.tpr
-rw-r--r-- 1 pdfco pdfco 484783632  April 22 12:26 nvt.trr
-rw-r--r-- 1 pdfco pdfco 72725876   April 22 14:23 nvt.xtc
-rw-r--r-- 1 pdfco pdfco 48075   April 22 09:37 posre.itp
-rw-r--r-- 1 pdfco pdfco 21027   April 22 09:45 pot.xvg
-rw-r--r-- 1 pdfco pdfco 13065   April 22 18:10 pres.xvg
-rw-r--r-- 1 pdfco pdfco 1815967 April 22 09:38 sol.gro
-rw-r--r-- 1 pdfco pdfco 1814139 April 22 09:42 sol_ions.gro
-rw-r--r-- 1 pdfco pdfco 12963   April 22 14:24 temperature.xvg
-rw-r--r-- 1 pdfco pdfco 12937   April 22 18:09 temp.xvg
-rw-r--r-- 1 pdfco pdfco 902275  April 22 09:42 topol.top

2) After using gmxcheck -f md.trr -m doc.tex:

Checking file md.trr
Reading frame 0 time 0.000
# Atoms 40313
Reading frame 2000 time 12000.000
WARNING: Incomplete frame: nr 2219 time 13314
Item #frames Timestep (ps)
Step 2219 6
Time 2219 6
Lambda 2219 6
Coords 2219 6
Velocities 2219 6
Forces 0
Box 2219 6

3) After loading npt.gro and md.trr by VMD, there is no problem.

Unfortunately, again,  I encountered with:

Program mdrun, VERSION 4.6.3
Source code file: /build/buildd/gromacs-4.6.3/src/gmxlib/trnio.c, line: 311

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


4) After using df -h

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

Please help me to solve this problem.