The error after gmxcheck is: Can not open file: md_0_1.trr The first .trr file was the output of mdrun: grompp -f md.mdp -c npt_6.gro -t npt_6.cpt -p topol.top -n index.ndx -o md_0_1.tpr mpirun -np 32 mdrun_mpi -deffnm md_0_1 -v
I just tried to get rerun energy but it failed, then searched in mailing list, found that one of the common problems is the size of .trr file. So tried to split it to 10 files with the size of 2G. This was done in unix. Then tried again to run rerun on the new resized .trr files. Rerun worked just on the first .trr and did not work for the rest of them. Would you please give me suggestions? Thanks. Sincerely, Shima -------------------------------------------- On Fri, 1/24/14, Justin Lemkul <[email protected]> wrote: Subject: Re: [gmx-users] Rerun error To: [email protected], "Shima Arasteh" <[email protected]> Date: Friday, January 24, 2014, 12:40 PM On 1/24/14, 1:56 PM, Shima Arasteh wrote: > > > > > > On Friday, January 24, 2014 9:09 PM, Shima Arasteh <[email protected]> wrote: > I tried > trjconv -f md_0_1.trr -s md_0_1.tpr -split 1000 -o md_0_1_new.trr > > My system does not recognize the md_0_1.trr file. oh........... :-( > Would you please help me? > Providing a single command does not help much. What does "does not recognize" mean? What is the *exact* error? How was md_0_1.trr generated in the first place and how does it relate to the other files shown in the commands below? -Justin > > > Sincerely, > Shima > > > > > On Friday, January 24, 2014 8:23 PM, Mark Abraham <[email protected]> wrote: > > You're using unix split? That could work for .trr under the right conditions, but apparently it is not. trjconv has a million different ways to split trajectories, so try them. Also chekc that your file system can handle files bigger than 2GB at all. > > Mark > > > > On Fri, Jan 24, 2014 at 5:40 PM, Shima Arasteh <[email protected]> wrote: > > Making a new folder didn't solve my problem unfortunately. >> >> The commands I ran are these: >> 1.Split files larger than 2G >> split -b 2097152000 md_0_1.trr -d >> >> The output files are: >> x00 >> x01 >> x02 >> . >> . >> . >> x10 >> >> >> Then: >> 2.grompp -f md.mdp -c npt_6.gro -t npt_6.cpt -p topol.top -o md_rerun_0.tpr -n index.ndx >> 3.mdrun -rerun x00.trr -s md_rerun_0.tpr -e md_rerun_0.edr -o md_rerun_0.trr -v >> >> >> >> >> >> >> Sincerely, >> Shima >> >> >> ________________________________ >> From: Mark Abraham <[email protected]> >> To: Shima Arasteh <[email protected]> >> Cc: "[email protected]" <[email protected]> >> Sent: Friday, January 24, 2014 7:19 PM >> >> Subject: Re: [gmx-users] Rerun error >> >> >> >> So there's nothing in it. Maybe mdrun over-write it according to Christian's theory, but since we don't know what your commands were, we're guessing... The extra 30 seconds of copy-pasting your commands from your terminal would have led to an answer by now! >> >> Mark >> >> >> >> On Fri, Jan 24, 2014 at 4:19 PM, Shima Arasteh <[email protected]> wrote: >> >> Last frame -1 time 0.000 >>> >>> # Atoms -1 >>> Last frame -1 time 0.000 >>> >>> >>> Item #frames Timestep (ps) >>> Step 0 >>> Time 0 >>> Lambda 0 >>> Coords 0 >>> Velocities 0 >>> Forces 0 >>> Box 0 >>> >>> >>> >>> >>> >>> Sincerely, >>> Shima >>> >>> >>> >>> ________________________________ >>> From: Mark Abraham <[email protected]> >>> To: Discussion list for GROMACS users <[email protected]>; Shima Arasteh <[email protected]> >>> Sent: Friday, January 24, 2014 6:43 PM >>> Subject: Re: [gmx-users] Rerun error >>> >>> >>> >>> >>> What does gmxcheck say about this files? >>> >>> Mark >>> >>> >>> >>> On Fri, Jan 24, 2014 at 3:49 PM, Shima Arasteh <[email protected]> wrote: >>> >>> Hi, >>>> >>>> I had a large .trr file, tried to do rerun on it. First I used split command and made 10 new .trr files with 2G in size. Then ran rerun on the first 2G.trr, but this does not work for the rest of trr files and I get the error: >>>> The number of atoms in trajectory (-1) doesn't match the input file. >>>> >>>> Would you please give me any suggestions? >>>> Thanks in advance >>>> >>>> >>>> >>>> Sincerely, >>>> Shima >>>> -- >>>> 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]. >>>> >>> >> -- ================================================== Justin A. Lemkul, Ph.D. 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 [email protected] | (410) 706-7441 ================================================== -- 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].
