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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
