[gmx-users] Rerun error

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Jan 24 19:56:05 CET 2014






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?



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 
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>> 
> 


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