# Gmx energy LJ (SR) Calculation

**URL:** <https://gromacs.bioexcel.eu/t/gmx-energy-lj-sr-calculation/9113>\
**Category:** User discussions\
**Created:** [May 8, 2024, 10:54pm UTC](https://gromacs.bioexcel.eu/t/gmx-energy-lj-sr-calculation/9113 "2024-05-08T22:54:14Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![seegert](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/seegert/32/3312_2.png) [@seegert](https://gromacs.bioexcel.eu/u/seegert)\
**Post date:** [May 8, 2024, 10:54pm UTC](https://gromacs.bioexcel.eu/t/gmx-energy-lj-sr-calculation/9113/1 "2024-05-08T22:54:14Z")

</div>

GROMACS version: 2022.3  
GROMACS modification: No

Hello,

I am looking at simple MD simulations of homogeneous liquid Argon to understand GROMACS’s parameters before moving onto more complex systems.

Currently, I am having an issue replicating the gmx energy LJ (SR) calculation. My total LJ calculation for all unique pairs should overestimate GROMACS’s, then by excluding pairs outside the cut-off and subtracting the potential shift be brought to GROMACS’s LJ (SR). However, my total LJ calculation _underestimates_ GROMACS’s immediately.

Could someone help me understand why based on the below discussion?

**Method**

- Using gmx trjconv to generate .gro files of the coordinates of n particles every ns of the 11 ns simulation;
- Reading the coordinates into Python and calculating the total LJ between all unique pairs at each ns frame

**Results**  
 ![Figure 1](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/6/62e7135b6b9e0c69657ca7e9635b00566ef121e7.png)

- The red points are my calculated total LJ for all unique pairs;
- The blue data is the LJ (SR);
- The green line is the LJ (SR) average + the Dispersion Correction;
- The orange data is the total Potential

**Thoughts**

- I compared the positive and negative contributions in my total LJ. The positive contributions are only about 50 kJ/mol, so I don’t think I am somehow overly including positive contributions
- Pairs outside the cut-off have negative energy, so excluding them would make my values less negative
- The shift, V(r\_cut-off), is negative, so subtracting it from contributions would make my values less negative

**Non-Default Parameters**

integrator = md  
dt = 0.001  
nsteps = 11000000

cutoff-scheme = verlet  
nstlist = 10  
pbc = xyz

vdw-modifier = Potential-shift  
rvdw = 1.0  
DispCorr = EnerPres

tcoupl = Nose-Hoover  
nsttcouple = 5  
tc-grps = system  
tau-t = 0.1  
ref-t = 117.33

Thanks!  
Tom