# How to extract the Potential Energy of Protein and Ligand from the Entire System after MD Simulation **URL:** \ **Category:** User discussions\ **Created:** [February 12, 2024, 1:25pm UTC](https://gromacs.bioexcel.eu/t/how-to-extract-the-potential-energy-of-protein-and-ligand-from-the-entire-system-after-md-simulation/8321 "2024-02-12T13:25:20Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![magic\_corn](https://avatars.discourse-cdn.com/v4/letter/m/3da27b/32.png) [@magic\_corn](https://gromacs.bioexcel.eu/u/magic_corn)\ **Post date:** [February 12, 2024, 1:25pm UTC](https://gromacs.bioexcel.eu/t/how-to-extract-the-potential-energy-of-protein-and-ligand-from-the-entire-system-after-md-simulation/8321/1 "2024-02-12T13:25:20Z")
GROMACS version: 2022.2 GROMACS modification: No Hello, dear GROMACS users! I would appreciate any assistance for a GROMACS beginner. I have constructed the entire system with a cell membrane + water + ligand + protein, and then proceeded with the MD simulation using the following mdp. integrator = md dt = 0.002 nsteps = 500000 nstxout = 50000 nstvout = 50000 nstfout = 50000 nstcalcenergy = 100 nstenergy = 1000 nstlog = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw\_switch = 1.0 rvdw = 1.2 coulombtype = PME rcoulomb = 1.2 ; tcoupl = Nose-Hoover tc\_grps = SOLU MEMB SOLV tau\_t = 1.0 1.0 1.0 ref\_t = 303.15 303.15 303.15 ; pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau\_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref\_p = 1.0 1.0 ; constraints = h-bonds constraint\_algorithm = LINCS continuation = yes ; nstcomm = 100 comm\_mode = linear comm\_grps = SOLU\_MEMB SOLV Afterwards, to extract the energy specific to the protein and ligand rather than the entire system, I performed the steps as follows. 1. gmx make\_ndx -f step8\_601.tpr -o index\_2.ndx (Here, select atoms for protein and ligand to create a new index.) 2. gmx trjcat -f step8\*.trr -o combined.trr 3. gmx convert-tpr -s step8\_601.tpr -n index\_2.ndx -o energy\_tpr.tpr 4. gmx trjconv -s energy\_tpr.tpr -f combined.trr -n index\_2.ndx -o group\_trajectory.trr 5. gmx mdrun -s energy\_tpr.tpr -rerun group\_trajectory.trr -deffnm rerun\_specific -nb gpu 6. gmx eneconv -f rerun\_specific.edr -o final\_energy.edr 7. gmx energy -f final\_energy.edr -o energy\_data.xvg Could there be a problem with my method? I would be grateful for your response. ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [February 14, 2024, 8:56am UTC](https://gromacs.bioexcel.eu/t/how-to-extract-the-potential-energy-of-protein-and-ligand-from-the-entire-system-after-md-simulation/8321/2 "2024-02-14T08:56:32Z")
It’s difficult to tell from just the commands alone, was there any specific issue you ran into when running the commands that you needed help with? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [February 14, 2024, 11:41am UTC](https://gromacs.bioexcel.eu/t/how-to-extract-the-potential-energy-of-protein-and-ligand-from-the-entire-system-after-md-simulation/8321/3 "2024-02-14T11:41:27Z")
> [@magic\_corn](#): > > Could there be a problem with my method? The only problem I will mention is not a technical one, but a theoretical one. Extracting individual energies of various components has no physical meaning. No force field is parametrized in such a way that the absolute potential energies are targeted. You can calculate the quantity as shown, but the results will not tell you anything.