Thanks for the reply, My main problem a syntax error as all of em are similar, but I get the languages confussed sometimes. This worked;
#!/bin/bash i=1 for ((i=1;x<=1322;i+=1)); do g_energy -f energy.edr -o ${i}.xvg << EOF ${i} EOF done for everything in the energy file based on indexed components. I had finally written b efore giving up #!/bin/bash i=1 for (i=1;x<=1322;i+=1); do g_energy -f traj_5.edr -o $i.xvg << EOF ${i} EOF done Which is just a python script. Thanky again Stephan Lloyd Watkins -------- Original-Nachricht -------- > Datum: Fri, 9 Mar 2012 11:47:09 -0700 > Von: Oliver Stueker <ostue...@gmail.com> > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > Betreff: Re: [gmx-users] Re:g_energy > Hi Stephan, > > Have a look at: > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts > > something like this should work: > ----------8><----------schnipp----------><8---------- > #!/bin/bash > for i in Temperature Pressure ; do > g_energy -f ener.edr -o ${i}.xvg << EOF > ${i} > > EOF > done > ----------8><----------schnapp----------><8---------- > > creating Temperature.xvg and Pressure.xvg assuming there are terms > named like this in your ener.edr file. > The braces around the i might not be necessary in this case, but don't > hurt either. > > Best, > Oliver > > On Fri, Mar 9, 2012 at 08:00, lloyd riggs <lloyd.ri...@gmx.ch> wrote: > > > > Dear All, > > > > Is there a way to either supress the interactive portion of g_energy and > print out everything listed, or pass it to something more automated? MY > problem, I spent an hour or three trying to just write an automated four > line shell or python script to extract all the terms listed based on index > files. > > > > The error comes as I can not pass a variable i once the interactive > portion of the g_energy is invoked (I get error $i, i '$i', "$i", etc.. does > not match a pattern or whatever as an error each time). Basically try > getting a few dozen terms from an energy file, times 20 to 100 necessary > runs... > > > > Sincerely, > > > > Stephan Lloyd Watkins > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists