[gmx-users] Making Commands Non-Interactive

[Alexander Bujotzek]

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