[gmx-users] Re:: Specified frame doesn't exist or file not seekable

[Florian Haberl]

Hi,

On Sunday, 15. June 2008 18:12, sudheer babu wrote:
> I am having the evidence that I have drawn RMSD plot for 7.25ns
> simulation, in rmsd.xvg file showed the values of the time(ps),
> mentioned in *trjconv command
>
> Im pasting my .mdp file
>
> title               =  dpt_prod
> constraints         =  hbonds
> integrator          =  md
> dt                  =  0.002
> nsteps              =  500000
> nstcomm             =  1
>
> ;output control statements
> nstxout             =  100
> nstlog              =  100
> nstenergy           =  100
> nstlist             =  10
> ~
> ~
>
> My idea of doing this trjconv command is by mistaken I have deleted
> 7thns .trr but I have that file in .xtc format, so I am trying to get
> 7ns file in .trr format for continue my simualation

see 
http://wiki.gromacs.org/index.php/Doing_Restarts

If you lost your trr file you can`t do exact restarts. The xtc file has no 
full precision information which would be therefore necessary.

Also you should upgrade gromacs to version 3.3.3, i think there s this xtc bug 
fixed.

>
> Thanks in advance.
>
> sudheer babu wrote:
> >* Hi all,
>
> *>*        I am having 7.25ns trajectory file , I am trying to pick up
> *>* 6250ps to 7250 ps  trajectory file from whole trajectory by using
> trjconv, *>* Command line is
> *>*     *trjconv  -f  7.25ns.xtc  -s  pr.tpr  -o 6.25_7.25_out.trr  -b
> *>* 6250  -e  7250
> *>*      selected  " system " for getting output
> *>*  it showed the following error
> *>* -----------------------------------------------------------------
> *>* Program trjconv, VERSION 3.3.1
> *>* Source code file: trxio.c, line: 635
> *>*
> *>* Fatal error:
> *>* Specified frame doesn't exist or file not seekable
> *>* -----------------------------------------------------------------------
> *
>
> >That sounds pretty specific to me. What's your evidence that the file is
> >seekable and these frames exist?
> >
> >Check that your .mdp file options should have caused XTC output to be
> >written in this time. Then look at a gmxdump of this .trr file.
> >
> >It's not relevant to the problem, but there's almost no value in writing
> >XTC input in .trr format on output.
> >
> >*  I have found few discussions in gmx-archives regarding this problem and
>
> *>* due to BUG in source code its showing error.
> *


Greetings,

Florian
-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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