[gmx-users] gromacs.org_gmx-users Digest, Vol 148, Issue 88

[Quyen V. Vu]

thanks for your replying,
I think if I type 8|9 then my index.ndx should not appear [systems] group (
it too large for my system)
And if I use index of LA and CL in index.ndx to get coordinate from xtc
file, I got message: Segmentation fault (core dumped)



> Hi,
>
> What do you think is wrong about the contents of the index group that was
> made?
>
> Mark
>
> On Tue, Aug 23, 2016 at 6:26 PM Quyen V. Vu <vuqv.phys at gmail.com> wrote:
>
> > Dear gromacs user,
> > my system contain such groups:
> >
> >   0 System              : 943920 atoms
> >   1 DNA                 :  3198 atoms
> >   2 LA                  :    76 atoms
> >   3 CL                  :   130 atoms
> >   4 Water               : 940516 atoms
> >   5 SOL                 : 940516 atoms
> >   6 non-Water           :  3404 atoms
> >   7 Other               :    76 atoms
> >   8 LA                  :    76 atoms
> >   9 CL                  :   130 atoms
> >  10 Ion                 :   130 atoms
> >  11 LA                  :    76 atoms
> >  12 CL                  :   130 atoms
> >  13 Water_and_ions      : 940646 atoms
> >
> > Now, I want to get index of La and CL ions then I type:
> >        gmx make_ndx -f em.gro -o index.ndx
> > at the make_ndx prompt I type: "8|9"
> > then in my index.ndx I get group [LA_CL], also get [system] group ( too
> > much index)
> > How can I use correct make_ndx?
> > Thank you.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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> >
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 23 Aug 2016 16:30:24 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org,      "gromacs.org_gmx-users"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Help with gmx make_ndx
> Message-ID:
>         <CAMNuMAT-Rhp_0keBZDSxdJaTLRqn4Cd+E4Gq747a8v23dqGDCA at mail.gmail.
> com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> What do you think is wrong about the contents of the index group that was
> made?
>
> Mark
>
> On Tue, Aug 23, 2016 at 6:26 PM Quyen V. Vu <vuqv.phys at gmail.com> wrote:
>
> > Dear gromacs user,
> > my system contain such groups:
> >
> >   0 System              : 943920 atoms
> >   1 DNA                 :  3198 atoms
> >   2 LA                  :    76 atoms
> >   3 CL                  :   130 atoms
> >   4 Water               : 940516 atoms
> >   5 SOL                 : 940516 atoms
> >   6 non-Water           :  3404 atoms
> >   7 Other               :    76 atoms
> >   8 LA                  :    76 atoms
> >   9 CL                  :   130 atoms
> >  10 Ion                 :   130 atoms
> >  11 LA                  :    76 atoms
> >  12 CL                  :   130 atoms
> >  13 Water_and_ions      : 940646 atoms
> >
> > Now, I want to get index of La and CL ions then I type:
> >        gmx make_ndx -f em.gro -o index.ndx
> > at the make_ndx prompt I type: "8|9"
> > then in my index.ndx I get group [LA_CL], also get [system] group ( too
> > much index)
> > How can I use correct make_ndx?
> > Thank you.
> > --
> > 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-request at gromacs.org.
> >
>
>
> ------------------------------
>
>