Analysis are normally performed locally on a workstation, i.e. copy back all the files from the supercomputer to your local directory.
A typical analysis tasks reads the trajectory (XTC) or energy (EDR) file, computes quantities, and produces data files that can be plotted or processed further, e.g. using Python scripts. A strength of Gromacs_ is that it comes with a wide range of tools that each do one particular analysis task well (see the `Gromacs manual`_ and the `Gromacs documentation`_).
If you just look at the output trajectory :file:`md.xtc` in VMD_ then you will see that the protein can be split across the periodic boundaries and that the simulation cell just looks like a distorted prism. You should recenter the trajectory so that the protein is at the center, remap the water molecules (and ions) to be located in a more convenient unitcell representation.
We will use the :ref:`gmx trjconv` tool in Gromacs to center and remap our system.
Tip
:program:`gmx trjconv` prompts the user with a number of questions that depend on the selected options. In the command line snippets below, the user input is directly fed to the standard input of :program:`trjconv` with the printf TEXT | gmx trjconv "pipe" construct. In order to better understand the command, run it interactively without the pipe construct and manually provide the required information.
Center (-center) on the Protein and remap all the molecules
(-pbc mol) of the whole System:
printf "Protein\nSystem\n" | gmx trjconv -s md.tpr -f md.xtc -center -ur compact -pbc mol -o md_center.xtc
It is often desirable to RMS-fit the protein on a reference structure (such as the first frame in the trajectory) to remove overall translation and rotation. In Gromacs, the :ref:`gmx trjconv` tool can also do more "trajectory conversion tasks". After (1) centering and remapping the system, we want to (2) RMS-fit (due to technical limitations in :program:`gmx trjconv` you cannot do both at the same time).
RMS-fit (-fit rot+trans) to the protein backbone atoms in
the initial frame (supplied in the TPR file) and write out the
whole System:
printf "Backbone\nSystem\n" | gmx trjconv -s md.tpr -f md_center.xtc -fit rot+trans -o md_fit.xtc
Visualize in VMD_:
vmd ../posres/posres.pdb md_fit.xtc
Note
If you don't have a :program:`vmd` command available on the command
line then launch VMD_, load the posres/posres.pdb file
(:menuselection:`File --> New Molecule...`), highlight your molecule 1
("em.pdb") and load the posres/md_fit.xtc trajectory into your
molecule 1, :menuselection:`File --> Load Data Into Molecule`. You
should see that the first frame (from the energy minimization) looks
as if the water is in a distorted box shape whereas all further frames
show a roughly spherical unit cell (the rhombic dodecahedron).