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My guess would be that for some reason (which I don't know),<br>your xtc file has not been written to disk completely.<br>You can check this by using gmxdump -cp on your checkpoint file<br>and looking at the size of the xtc file.<br><br>Berk<br><br>> Date: Fri, 7 Aug 2009 10:19:35 +0200<br>> From: qiaobf@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] question about mdrun -append<br>> <br>> Hi all,<br>> <br>> I meet one problem when I am using mdrun -append. In some cases, the<br>> following error information happens, and mdrun is halted<br>> *************************************************<br>> Program mdrun, VERSION 4.0.5<br>> Source code file: checkpoint.c, line: 1248<br>> Fatal error:<br>> Truncation of file T298.xtc failed.<br>> *************************************************<br>> Line 1248 in checkpoint.c is the inner loop as follows<br>> *********************************************************************************<br>> if(bAppendOutputFiles) {<br>> for(i=0;i<nfiles;i++) {<br>> if(0 !=<br>> truncate(outputfiles[i].filename,outputfiles[i].offset) ) {<br>> gmx_fatal(FARGS,"Truncation of file %s<br>> failed.",outputfiles[i].filename);<br>> }<br>> }<br>> }<br>> *********************************************************************************<br>> <br>> But I don't know how to solve it. Please give some suggestions! Thanks a<br>> lot!<br>> <br>> The following script is used<br>> grompp -f T298.mdp -c pre2.gro -p system.top -o T298<br>> mpirun -np 40 mdrun -npme 12 -deffnm T298 -maxh 23.5<br>> mpirun -np 40 mdrun -npme 12 -deffnm T298 -maxh 23.5 -cpi T298.cpt -append<br>> <br>> regards,<br>> Baofu Qiao<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
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