On 1/19/18 11:45 AM, ZHANG Cheng wrote:
Dear Gromacs, I run Gromacs on our cluster, and use this command to continue my run from last checkpoint. gmx mdrun -deffnm md_0_1 -cpi -append Each new run will generate four log files: md_0_1.e<job_ID> md_0_1.o<job_ID> md_0_1.pe<job_ID> md_0_1.po<job_ID> Gradually, I have thousands of log files. So I used these commands to delete all of them in one go, : rm md_0_1.e* rm md_0_1.o* rm md_0_1.pe* rm md_0_1.po* I thought the checkpoint information is only stored in md_0_1.cpt, md_0_1_prev.cpt and some files like md_0_1_step47660830.cpt, which I did not delete. However, after deleting all the log files, and then started a new run, I was told: Fatal error: File appending requested, but 1 of the 4 output files are not present or are named differently So it seems that the checkpoint information is also in one of those md_0_1.e<job_ID>, md_0_1.o<job_ID>, md_0_1.pe<job_ID>, md_0_1.po<job_ID> files?
The checkpoint file specifies all the names of the mdrun output files that you're trying to append to. By removing md_0_1.e* you have deleted md_0_1.edr, which stores your energy data. mdrun can't append to a file that isn't there. I suggest you be more judicious in your shell globbing to avoid removing important output.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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.
