Thank you. 2015-09-17 12:37 GMT+01:00 Mark Abraham <mark.j.abra...@gmail.com>:
> Hi, > > Yes. Further options at > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts > > Mark > > On Thu, Sep 17, 2015 at 1:04 PM Dawid das <add...@googlemail.com> wrote: > > > O'right, I have figured that out myself. Just use text file like data.txt > > with two lines: > > 1 > > 1 > > > > and redirect it: g_rms [options] < data.txt > > > > 2015-09-17 11:32 GMT+01:00 Dawid das <add...@googlemail.com>: > > > > > Dear Gromacs Experts, > > > > > > Let's say that for some reasons I don't want to specify the atom group > > > when g_rms (or other module) prompts me to do so. > > > So I do not want to see this: > > > > > > Select group for RMSD calculation > > > Group 0 ( System) has 38387 elements > > > Group 1 ( Protein) has 3470 elements > > > Group 2 ( Protein-H) has 1772 elements > > > Group 3 ( C-alpha) has 217 elements > > > Group 4 ( Backbone) has 653 elements > > > Group 5 ( MainChain) has 869 elements > > > Group 6 ( MainChain+Cb) has 1065 elements > > > Group 7 ( MainChain+H) has 1076 elements > > > Group 8 ( SideChain) has 2394 elements > > > Group 9 ( SideChain-H) has 903 elements > > > Group 10 ( Prot-Masses) has 3461 elements > > > Group 11 ( non-Protein) has 34917 elements > > > Group 12 ( Water) has 34845 elements > > > Group 13 ( SOL) has 34845 elements > > > Group 14 ( non-Water) has 3542 elements > > > Group 15 ( Ion) has 72 elements > > > Group 16 ( NA) has 37 elements > > > Group 17 ( CL) has 35 elements > > > Group 18 ( Water_and_ions) has 34917 elements > > > Group 19 ( Chromophore) has 37 elements > > > Select a group: 1 > > > Selected 1: 'Protein' > > > > > > and I want to specify this Group 1 (Protein) in my command, e.g. > > > g_rms -s ../npt-md2.tpr -f ../npt-md2.xtc -tu ns -b 0 -e 100 -n > > > ../index.ndx -o rmsd-0-100.xvg > > > -some_option 1 > > > Is it possible? > > > > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.