[gmx-users] Rerun error
Mark Abraham
mark.j.abraham at gmail.com
Mon Jan 27 19:51:04 CET 2014
Yes. You need to read the positions to do a rerun. To do that, you need to
be able to read the file.
Mark
On Mon, Jan 27, 2014 at 7:25 PM, Shima Arasteh
<shima_arasteh2001 at yahoo.com>wrote:
> Does it mean that doing rerun on current md_0_1.trr file is impossible,
> unless it is transfered to a cluster or a more powerful system?
>
>
> Sincerely,
> Shima
>
>
>
> On Sunday, January 26, 2014 11:50 AM, Mark Abraham <
> mark.j.abraham at gmail.com> wrote:
> Hi,
>
> Thanks for the full description. It seems like your file system cannot
> handle files over 2gb even for splitting, which is not surprising, because
> the limitation is based on the use of a 32-bit integer. You should get
> access to a better file system, where maybe your file can be read. You may
> wish to consider the advice at
>
> http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume
>
> Mark
> On Jan 26, 2014 8:34 AM, "Shima Arasteh" <shima_arasteh2001 at yahoo.com>
> wrote:
>
> > 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
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu
> > | (410) 706-7441
>
> >
> > ==================================================
> >
> >
> > --
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