18 dec 2012 kl. 09.30 skrev Tsjerk Wassenaar: > Hi KT, > > If you mean concatenating frames in .gro files, you can use trjcat or just > cat. If you mean merging the coordinates, it's a wee bit more complicated. > Since you also ask for top files, I guess that's the case. Here's a snippet > of python code that will do the trick: > > #!/usr/bin/env python > > import sys > > f = [open(i).readlines() for i in sys.argv[1:]] > print "Merged gro file\n%5d" % (sum([len(i) for i in f]) - 3*len(f)) > print "".join(["".join(i[2:-1]) for i in f]), > print f[0][-1] > > > For the top files, it is necessary to ensure all the moleculetypes are > #included, and that the [ molecules ] listing under [ system ] has the > right number and order of the molecules in the merged gro file. There's no > tool for that that I know of.
In principle you could use grompp for checking that. It would print out a heap of warinngs/notes/errors if structure file and topology don't match. Erik > > Cheers, > > Tsjerk > > > On Tue, Dec 18, 2012 at 6:18 AM, Kieu Thu Nguyen <kieuthu2...@gmail.com>wrote: > >> Dear All, >> >> I don't know which tools used to merge 2 files .gro, 2 files .top ? >> Can i use trjcat ? >> >> Thanks ! >> KT >> -- >> 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 >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Biocomputing Group > Department of Biological Sciences > 2500 University Drive NW > Calgary, AB T2N 1N4 > Canada > -- > 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 ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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
