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Hi Berk, Thanks for your reply! The result of "gmxdump -cp T298.cpt" is given as follows (the long list of x, v, E is not shown) ************************************** number of output files = 4 output filename = T298.log file_offset_high = 0 file_offset_low = 7228659 output filename = T298.trr file_offset_high = 0 file_offset_low = 0 output filename = T298.xtc file_offset_high = 0 file_offset_low = -2020699160 output filename = T298.edr file_offset_high = 0 file_offset_low = 13270732 ************************************** But I don't know what this number means! On the other hand, another system, which can be continued using "mdrun -cpi T298.cpt", gives the following result of "gmxdump -cp T298.cpt" *************************************** number of output files = 4 output filename = T298.log file_offset_high = 0 file_offset_low = 7066641 output filename = T298.trr file_offset_high = 0 file_offset_low = 0 output filename = T298.xtc file_offset_high = 0 file_offset_low = 2144960064 output filename = T298.edr file_offset_high = 0 file_offset_low = 19540796 *************************************** It seems that the difference is: there is a negative number (-2020699160) in the former case. So what should I do? regards, Berk Hess wrote: My guess would be that for some reason (which I don't know), your xtc file has not been written to disk completely. You can check this by using gmxdump -cp on your checkpoint file and looking at the size of the xtc file.BerkDate: Fri, 7 Aug 2009 10:19:35 +0200 From: qia...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] question about mdrun -append Hi all, I meet one problem when I am using mdrun -append. In some cases, the following error information happens, and mdrun is halted ************************************************* Program mdrun, VERSION 4.0.5 Source code file: checkpoint.c, line: 1248 Fatal error: Truncation of file T298.xtc failed. ************************************************* Line 1248 in checkpoint.c is the inner loop as follows ********************************************************************************* if(bAppendOutputFiles) { for(i=0;i<nfiles;i++) { if(0 != truncate(outputfiles[i].filename,outputfiles[i].offset) ) { gmx_fatal(FARGS,"Truncation of file %s failed.",outputfiles[i].filename); } } } ********************************************************************************* But I don't know how to solve it. Please give some suggestions! Thanks a lot! The following script is used grompp -f T298.mdp -c pre2.gro -p system.top -o T298 mpirun -np 40 mdrun -npme 12 -deffnm T298 -maxh 23.5 mpirun -np 40 mdrun -npme 12 -deffnm T298 -maxh 23.5 -cpi T298.cpt -append regards, Baofu Qiao _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php_________________________________________________________________ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx |
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
