[gmx-users] extracting trajectory using trjconv

[Chenyu Liu]

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
>> --
>> 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.
>>
>