Analyzing MD Simulations

Adapted using tutorial from "http://www.mdtutorials.com/gmx/lysozyme/index.html"

All simulation analysis is done using the HCC cluster.

1. Once the simulation is done running, the first step is to convert the trajectory. Do this by running “gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center”.
   1. The -pbc flag corrects for periodicity and may need to be changed based on specific protein simulations. Instructions for changing this flag can be found in the GROMACS manual (https://manual.gromacs.org/2020/manual-2020.pdf).
2. Once the .xtc file is created, many different analyses can be completed using the same general commands. The GROMACS manual is the best place to find useful commands, as well as a list of analyses that can be completed.
3. Several of the most common analyses are RMSD, radius of gyration and solvent accessible surface area (SASA). The commands for these analyses are below.

RMSD

1. Run the command “gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns”, making sure that input files -s and -f match exactly the naming conventions you used previously. Input “4” and “4” when prompted.
   1. Outputs RMSD values in ns for the duration of the simulation.

Radius of Gyration

1. Run the command “gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg”. Input “1” when prompted.
   1. Outputs radius of gyration values in ps for the duration of the simulation.

SASA

1. Run the command “gmx sasa -s md_0_1.tpr -f traj1.xtc -tu ns -o sasa.xvg”, inputing “1” when prompted.
   1. Outputs SASA values in ns for the duration of the simulation.