[gmx-users] extracting trajectory using trjconv

[Chenyu Liu]

Unfortunately, I have not seen similar situation before. The index could be
overlapping, for example: Protein, Non protein, water and chloride ions
where Non protein include the water and chloride ions. But I have not seen
the situation where the same name appears multiple times. I think you
should look into topology file to modify and solve the problem.
Good luck with that,
Chenyu

On Tue, Oct 1, 2019 at 7:24 PM Hadi Rahmaninejad <ha.rahmaani at gmail.com>
wrote:

> Thank you Chenyu, but I thought there should be option for index file,
> however when I wanted to create an index file, for some reason my molecule
> appears two times and it gives me an error message of "having multiple same
> names" and cannot create the index file. Do you have any suggestions?
>
> Best,
> Hadi
>
> On Tue, Oct 1, 2019 at 5:14 PM Chenyu Liu <liu00554 at umn.edu> wrote:
>
> > I noticed that there are extra '*'s in my post, please ignore that (which
> > comes from the bold font I used
> > this should look good
> >
> > gmx_mpi energy -f npt.edr -o density.xvg <<EOF
> > Density
> > (Input2.....)
> > EOF
> >
> >
> > On Tue, Oct 1, 2019 at 4:11 PM Chenyu Liu <liu00554 at umn.edu> wrote:
> >
> > > Hi Hadi,
> > >
> > > You can do this kind of option in this way (here is a part of my .pbs
> > file
> > > for submitting jobs):
> > >
> > >
> > > *gmx_mpi energy -f npt.edr -o density.xvg <<EOFDensity*
> > >
> > > *(Input2.....)EOF*
> > >
> > > (Reference:
> > > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
> )
> > > The option is between the two 'EOF's. You need to run a few runs
> > > interactively to figure out what the inputs should be. Also, if you
> want
> > to
> > > do the same operation for multiple files, I would suggest checking out
> > bash
> > > programming for doing that.
> > > I hope this will help you.
> > >
> > > Chenyu Liu
> > >
> > > On Tue, Oct 1, 2019 at 3:46 PM Hadi Rahmaninejad <
> ha.rahmaani at gmail.com>
> > > wrote:
> > >
> > >> Hello Gromacs Users,
> > >>
> > >> I am going to use "trjconv" to extract trajectory from a .trr file.
> Here
> > >> is
> > >> my command:
> > >> "gmx trjconv -f x.trr -s x.gro -o frames.gro"
> > >> then it gives me the options to choose my group, but I wanna it choose
> > for
> > >> me automatically, as I am going to extract from a lot of simulations
> > using
> > >> a loop. In another word, I need to give it the name of my projectile
> > >> molecule in the command line. Can anybody help me with this?
> > >>
> > >> Thank you in advance,
> > >> Hadi
> > >> --
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