On 4/26/14, 4:54 AM, Andrew Bostick wrote:
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.
Your file system probably doesn't support files larger than 2GB; your .trr is exactly that size. Reduce your output frequency or do your simulation in shorter increments of time.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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 gmx-users-requ...@gromacs.org.