Analysis

Trajectory conversion

Gromacs can work with a number of trajectory file formats. The two most important are TRR Files and XTC Files. You can get more information on trajectory file types (popup). All trajectory conversions can be performed with the Gromacs tool trjconv.
Create a trajectory file containing only protein atoms (select the protein group):

gmx trjconv -f md.xtc -s md.tpr -o md_protein.xtc -center -ur compact -pbc mol

We also need a *.gro or *.pdb file that contains the exact particles as the trajectory, so other programs know how to interpret the numbers in the trajectory. It is possible to dump the first frame at time 0 into a *.pdb file:

gmx trjconv -f md.xtc -s md.tpr -o md_protein.pdb -center -ur compact -pbc mol -dump 0

For many Gromacs analysis tools it is handy to have a trajectory input file (*.tpr) with the exact same particles (protein atoms in this case), as it contains explicit information on bonds and enables Gromacs tools to handle artifacts that are produced by molecules that cross periodic boundary conditions:

gmx convert-tpr -s md.tpr -o md_protein.tpr

Looking at the trajectory with VMD

After correction of the periodic boundaries, you can look the trajectory via VMD by the following command:

vmd md_protein.pdb md_protein.xtc

As only the protein is visible, first choose the New Cartoon representation for [KIGAKI]₃ as drawing method. For the coloring method, use the Secondary Structure. Now, you can follow the MD simulation via the main window of VMD. But the problem is that VMD does not update the secondary structure. Therefore, you need a free available TCL script. Load the following script into your working directory: sscache.tcl

Next, open the Extensions > Tk consule and type the following the commands to source and to activate the script (ensure that script is located in the directory where you open VMD):

source sscache.tcl start_sscache 0

The number 0 means that you start the updating of the secondary structure for the molecule 0 in VMD, in which you can have more than one molecule if load more structures. To stop the script, then type in the Tk consule:

stop_sscache 0

Depending on the size of system and MD simulation length, the script can slow down VMD, therefore, it is recommended that the script is only activated for one moelcule.

Finally, save the visualization state via File > Save Visualization State and choose the name with the ending *.vmd (for instance, md_protein.vmd). If you open this file with an editor, you will see that is a text file with all visualization settings (representations, colors, labels, display etc.). There is also a part with loading of the pdb file and after that, the tractory file. To open the md_protein.vmd, you have to use the following command:

vmd -e md_protein.vmd

The flag -e means for VMD to read a text file which can contain a tcl script or a visualization state. Here, it is also recommended to open this file in the directory where the corresponding files (md_protein.pdb and md_protein.xtc) are located. For more information and tutorials for VMD, consider this website of the developers.