Thanks Justin, this is great. On Tue, Jul 17, 2012 at 5:07 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/17/12 4:57 PM, Andrew DeYoung wrote: >> >> Hi Justin, >> >> I am just curious, do you have experience writing such a shell script to >> iterate over the index files (one per frame)? I am just curious, because >> I >> have been trying this, and I have found it very difficult to do using >> bash. >> Do you use a different shell language? >> >> Also, I wonder if anyone has ever posted such a shell script on this list. >> When I look through the archives, I don't see one, but I could be wrong. >> > > Assume we have 100 groups of arbitrary size and a fixed group (index group > 0) in the index file to which we wish to calculate hydrogen bonds. Then > assume we have 100 separate files (from trjconv -sep or whatever else) > numbered sequentially, i.e. conf1.gro, conf2.gro...conf100.gro. A simple > bash script that runs through the index groups corresponding to each of > these coordinate files would be something like: > > #!/bin/bash > > for i in {1..100} > do > echo 0 $i | g_hbond -s topol.tpr -f conf$i.gro -n index.ndx > done > > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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
-- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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