[gmx-users] extracting trajectory using trjconv

[Chenyu Liu]

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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