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 <[email protected]> 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 >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > Alexander Bujotzek > Zuse Institute Berlin > Computational Drug Design Group > Tel. : +49 30 84185-234 > eMail: [email protected] > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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 _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
