[gmx-users] Rerun error

Shima Arasteh shima_arasteh2001 at yahoo.com
Mon Jan 27 19:26:39 CET 2014 

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
>  >>>>
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>  >>>>
>  >>>
>  >>
>
>  --
>  ==================================================
>
>  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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