# Simulation won't fully run pair searching **URL:** \ **Category:** User discussions\ **Created:** [June 30, 2023, 10:25pm UTC](https://gromacs.bioexcel.eu/t/simulation-wont-fully-run-pair-searching/6724 "2023-06-30T22:25:39Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![inigma91](https://avatars.discourse-cdn.com/v4/letter/i/c4cdca/32.png) [@inigma91](https://gromacs.bioexcel.eu/u/inigma91)\ **Post date:** [June 30, 2023, 10:25pm UTC](https://gromacs.bioexcel.eu/t/simulation-wont-fully-run-pair-searching/6724/1 "2023-06-30T22:25:39Z")
GROMACS version: version 2019 GROMACS modification: No Here post your question I would like to calculate the interaction energy between a ligand (LIG) and a residue (r36). I have grouped LIG and r36. However, the gmx energy does run full frame. WARNING: Incomplete frame: nr 1257 time 12570 NOTE: 32 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Below is my mdp. title = Protein-ligand complex MD simulation ; Run parameters integrator = md ; leap-frog integrator nsteps = 25000000 ; (50 ns) dt = 0.002 ; 2 fs ; Output control nstenergy = 5000 ; save energies every 10.0 ps nstlog = 5000 ; update log file every 10.0 ps nstxout-compressed = 5000 ; save coordinates every 10.0 ps energygrps = LIG\_r\_36 ; Bond parameters continuation = yes ; continuing from NPT constraint\_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds to H are constrained lincs\_iter = 1 ; accuracy of LINCS lincs\_order = 4 ; also related to accuracy ; Neighbor searching and vdW cutoff-scheme = Verlet ns\_type = grid ; search neighboring grid cells nstlist = 20 ; largely irrelevant with Verlet rlist = 1.2 vdwtype = cutoff vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics rcoulomb = 1.2 pme\_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein\_SAM\_LIG Water\_and\_ions ; two coupling groups - more accurate tau\_t = 0.1 0.1 ; time constant, in ps ref\_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau\_p = 2.0 ; time constant, in ps ref\_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction is not used for proteins with the C36 additive FF DispCorr = no ; Velocity generation gen\_vel = no ; continuing from NPT equilibration (END) ---
**Author:** ![XiaoDingdang](https://avatars.discourse-cdn.com/v4/letter/x/a9a28c/32.png) [@XiaoDingdang](https://gromacs.bioexcel.eu/u/XiaoDingdang)\ **Post date:** [August 21, 2025, 8:39am UTC](https://gromacs.bioexcel.eu/t/simulation-wont-fully-run-pair-searching/6724/2 "2025-08-21T08:39:55Z")
I’ve also encountered this problem.May I ask if you’ve solved it? ---
**Author:** ![al42and](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/al42and/32/1393_2.png) [@al42and](https://gromacs.bioexcel.eu/u/al42and)\ **Post date:** [August 21, 2025, 8:53am UTC](https://gromacs.bioexcel.eu/t/simulation-wont-fully-run-pair-searching/6724/3 "2025-08-21T08:53:08Z")
See here: [Simulation won’t fully run pair searching - #2 by hess](https://gromacs.bioexcel.eu/t/simulation-won-t-fully-run-pair-searching/6746/2) ---
**Author:** ![XiaoDingdang](https://avatars.discourse-cdn.com/v4/letter/x/a9a28c/32.png) [@XiaoDingdang](https://gromacs.bioexcel.eu/u/XiaoDingdang)\ **Post date:** [August 21, 2025, 9:40am UTC](https://gromacs.bioexcel.eu/t/simulation-wont-fully-run-pair-searching/6724/4 "2025-08-21T09:40:04Z")
I encountered this problem during the MD simulation. There was no error message, but the simulation just stopped.May I ask why this is the case?