Calculate distance between two groups of atoms of trajectory

Gromacs:

1. Prepare your input files:

   • Make sure you have a GROMACS-compatible topology file (e.g., .top) and a trajectory file (e.g., .xtc or .trr) that contains the trajectory of your simulated system.

2. Define the two groups of atoms:

   • Identify the specific atom indices that represent the two groups you want to calculate the distance between. You can find this information in the topology file or use GROMACS utilities like "gmx editconf" to visualize your system and assign atom groups based on their indices.

3. Trajectory analysis using "gmx distance":

   • GROMACS provides a built-in utility called "gmx distance" that can calculate distances between atom groups across your trajectory. You can use this tool to measure the distance between the selected atoms over time.

   • The command may look something like this:

     gmx distance -f trajectory.xtc -s topol.tpr -n index.ndx -select "group1" -select "group2" -oav distance.xvg

     Here, "trajectory.xtc" is the trajectory file, "topol.tpr" is the GROMACS run input file, "index.ndx" is the index file containing the atom group selections, and "group1" and "group2" are the names of the atom groups you defined in the index file. The "-oav" flag specifies that the output will be stored in an .xvg file, which you can plot or analyze further.

4. Visualize and analyze the output:

   • Once you have the distance.xvg file, you can plot the data or perform additional analysis using tools like xmgrace or Python libraries (e.g., Matplotlib) to obtain meaningful insights from your calculated distances.

VMD:

1. Open your molecular structure and trajectory in VMD:

   • Launch VMD and load your molecule's structure file (e.g., PDB or DCD) and the corresponding trajectory file (e.g., DCD or XTC) by using the "File" menu and selecting "New Molecule" and "Load Trajectory," respectively.

2. Create selections for the two groups of atoms:

   • Go to "Graphics" > "Representations" to open the "Graphical Representations" window.

   • In the "Graphical Representations" window, click on the "Create" tab.

   • Use the selection text to define the two groups of atoms. For example, if you want to calculate the distance between two residues with indices 10 and 20, you can create selections like:

     set group1 [atomselect top "resid 10"]

     set group2 [atomselect top "resid 20"]

3. Measure the distance between the groups in each frame:

   • Open the "Extensions" menu and select "Analysis" > "Measure Distances."

   • In the "Measure Distances" window, select the two atom selections you created earlier (group1 and group2) from the drop-down menus for "Reference" and "Target," respectively.

   • Click on the "Apply" button to calculate the distance between the two groups in each frame of the trajectory.