[gmx-users] Rerun error

[Shima Arasteh]

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 <jalemkul at vt.edu> wrote:

 Subject: Re: [gmx-users] Rerun error
 To: gmx-users at gromacs.org, "Shima Arasteh" <shima_arasteh2001 at yahoo.com>
 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
 <shima_arasteh2001 at yahoo.com>
 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
 <mark.j.abraham at gmail.com>
 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 <shima_arasteh2001 at yahoo.com>
 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 <mark.j.abraham at gmail.com>
 >> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
 >> Cc: "gmx-users at gromacs.org"
 <gmx-users at gromacs.org>
 >> 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
 <shima_arasteh2001 at yahoo.com>
 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 <mark.j.abraham at gmail.com>
 >>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>;
 Shima Arasteh <shima_arasteh2001 at yahoo.com>
 >>> 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
 <shima_arasteh2001 at yahoo.com>
 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 gmx-users-request at gromacs.org.
 >>>>
 >>>
 >>
 
 -- 
 ==================================================
 
 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow
 
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
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 jalemkul at outerbanks.umaryland.edu
 | (410) 706-7441
 
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