[gmx-users] extracting trajectory using trjconv

[Hadi Rahmaninejad]

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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