[gmx-users] Making Commands Non-Interactive

[Tsjerk Wassenaar]

Cool. You can also write a python script to generate and execute your
C-code, which you then wrap with Java to be executed through Ruby...
etc. Erik, can you maybe give the assembly solution?

:p

Tsjerk

On Mon, Oct 5, 2009 at 10:15 AM, Alexander Bujotzek <bujotzek at zib.de> wrote:
> I once wrote some lines of adventurous C-code to get an observable of
> choice from g_energy without typing the observable index myself... this
> may also be applied to trjconv I think.
>
> string genergyCall = "g_energy -f " + myEdrFile + " -o " + myXvgFile + "
> &> /dev/null";
> string energyObs = "8"; // e.g. potential
>
> FILE *fpipe;
> fpipe = popen(genergyCall.c_str(),"w");
> fwrite(energyObs.data(), 1, 1, fpipe); // tell g_energy what to write
> pclose(fpipe);
>
> If you want to pipe more stuff to the program you are calling, the buffer
> size of fwrite has to be increased.
> So you might put this into a minimal C-program and start that
> non-interactive with qsub or whatever.
>
>
>> Dear GMX Users,
>>
>> I ask this question in this mailing list since probably a user have
>> already encountered this similar problem. I would like to  post-process my
>> trajectory with the command trjconv (in mpi mode). For this I use the
>> following shell command:
>>
>> echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi
>> -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o
>> ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0
>> ("System")
>>
>> It works but since my simulations is very long (> 300ns) the command stops
>> in the middle of the trajectory before to finish the process ( i suspect a
>> time limit for using the interactive mode). So i would like to use a
>> script to do the task. How to pass the choice 0 in the script (i.e.
>> equivalent to the echo 0). I use a bash shell and the command qsub to
>> launch a mpi job.
>>
>> I have tried to adapt the examples available in the GMX website with a
>> text file as suggested by the author in GROMACS site with no success.
>>
>> Thank you again for your help
>>
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>
>
> --
> Alexander Bujotzek
> Zuse Institute Berlin
> Computational Drug Design Group
> Tel. : +49 30 84185-234
> eMail: bujotzek at zib.de
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623