[gmx-users] curious 'File not found' error

[David van der Spoel]

On Mon, 6 Jan 2003, Luciane Vieira de Mello wrote:

>Thanks Daan, but that's not it.  It looks like it is the file size issue
>after all.
>
>Our kernel is 2.4.7-10.  Is that old enough to have these problems?
>
>Any thoughts in general about how to avoid this kind of problem when we
>simulate large (interesting) proteins?

First of all use .xtc files, that saves you a factor of three in
diskspace, or delays the 2Gb problem by a factor of 3. Also, check how
often you save velocities and forces, you may not want to have them that
often.

Finally, upgrade your kernel...

>Thanks
>
>Luciane
>
>
>+-------------------------------------------------------------------------+
>|                  Dra. Luciane Vieira de Mello Rigden                    |
>| e-mail: mello at cenargen.embrapa.br                                       |
>| Embrapa Recursos Geneticos e Biotecnologia                              |
>| Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
>| PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
>| 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
>+-------------------------------------------------------------------------+
>
>
>
>On Mon, 6 Jan 2003, Daan Virtual wrote:
>
>>
>> Lucy
>>
>> I notice your file is -rw-------
>>
>> type
>> chmod 777 yourfilename
>>
>> and then try again
>>
>> Daan
>>
>> On Mon, 6 Jan 2003, Luciane Vieira de Mello wrote:
>>
>> > Hi
>> >
>> > Thanks for that tip Rainer.  What's the solution if my file is on the
>> > local hard disk - no nfs involved, presumably?
>> >
>> > Luciane
>> >
>> >
>> > +-------------------------------------------------------------------------+
>> > |                  Dra. Luciane Vieira de Mello Rigden                    |
>> > | e-mail: mello at cenargen.embrapa.br                                       |
>> > | Embrapa Recursos Geneticos e Biotecnologia                              |
>> > | Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
>> > | PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
>> > | 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
>> > +-------------------------------------------------------------------------+
>> >
>> >
>> >
>> > On Mon, 6 Jan 2003, Rainer Boeckmann wrote:
>> >
>> > > this may be due to an old NFS-version. As David pointed out two days ago, NFS3
>> > > supports files >2GB...
>> > > rainer
>> > >
>> > > Luciane Vieira de Mello wrote:
>> > >
>> > > > Hi everyone
>> > > >
>> > > > When I try to look at my trajectory
>> > > >
>> > > > ngmx -s xxx.tpr -f traj.trr
>> > > >
>> > > > I get this error
>> > > >
>> > > > Fatal error: File traj.trr not found
>> > > >
>> > > > even though the file is patently there
>> > > >
>> > > > -rw-------    1 mello    desenv   2719735808 Jan  6 09:35 traj.trr
>> > > >
>> > > > I get the same problem with a different large file when I try to restart a
>> > > > trajectory.
>> > > >
>> > > > Is this some problem with Linux file size, or something different?
>> > > >
>> > > > Many thanks in advance
>> > > >
>> > > > Luciane
>> > > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿà›î±ê왨¥Šx%ŠË`›î±êìþ
>> > > 虧,þŠà†ÛiÿÿðÃஉšrÏè®æj)fjåŠËbú?‚lÿºÇ«°ù^jǝ¢í¦‹-þéÿ²æìr¸›z·ª¹ë-²Ú-…éb²ßÔ±ëa{0Š{^­öœzŠìzwb¶Ú ›î±êìþ·ª¹ë-þ
>> > > 虧,þŠà
>> > >
>> >
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>>
>> Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
>> Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
>> Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
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