# Unexplained calculation stalling during density fit **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters, mdrun-performance, density-fit\ **Created:** [July 28, 2025, 12:33pm UTC](https://gromacs.bioexcel.eu/t/unexplained-calculation-stalling-during-density-fit/12449 "2025-07-28T12:33:23Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![YannLefrancois](https://avatars.discourse-cdn.com/v4/letter/y/dbc845/32.png) [@YannLefrancois](https://gromacs.bioexcel.eu/u/YannLefrancois)\ **Post date:** [July 28, 2025, 12:33pm UTC](https://gromacs.bioexcel.eu/t/unexplained-calculation-stalling-during-density-fit/12449/1 "2025-07-28T12:33:23Z")
GROMACS version: 2024.4=mpi\_openmpi\_cuda\_he6b8466\_0 (conda distribution) GROMACS modification: Yes/No I’m trying to do density fitting, following the bioexcel webinar #82, when i look at my performance log I see this ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/097ac3db68d65bf53d34759f77537546517348fb.png) 82% of the time has been spend on “rest”, not sure what it is exactly i have nothing else running on my workstation, i dont know what is stalling my computation so much here is my mdp file ; Run parameters integrator = md ; leap-frog integrator nsteps = 1500000 ; 2 \* 500000 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; suppress bulky .trr file by specifying nstvout = 0 ; 0 for output frequency of nstxout, nstfout = 0 ; nstvout, and nstfout nstenergy = 5000 ; save energies every 10.0 ps nstlog = 5000 ; update log file every 10.0 ps nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps compressed-x-grps = System ; save the whole system ; Bond parameters continuation = yes ; Restarting after NPT constraint\_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs\_iter = 1 ; accuracy of LINCS lincs\_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ; Buffered neighbor searching ns\_type = grid ; search neighboring grid cells nstlist = 200 ; 20 fs, largely irrelevant with Verlet scheme rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme\_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = RNA Water\_and\_Ions ; two coupling groups - more accurate tau\_t = 1 1 ; time constant, in ps ref\_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = C-rescale ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau\_p = 5.0 ; 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 DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen\_vel = no ; Velocity generation is off density-guided-simulation-active = true ; Activate density-guided simulations. density-guided-simulation-reference-density-filename = density.mrc density-guided-simulation-group = RNA ; Similarity measure between densities: inner-product, relative-entropy, or cross-correlation density-guided-simulation-similarity-measure = relative-entropy density-guided-simulation-force-constant = 10e3 ; The scaling factor for forces (can be negative) ; Atom amplitude for spreading onto grid: unity, mass, or charge density-guided-simulation-atom-spreading-weight = mass density-guided-simulation-gaussian-transform-spreading-width = 0.8 ; nm density-guided-simulation-nst = 100 density-guided-simulation-normalize-densities = true ; Normalize the sum of density voxel values to one density-guided-simulation-shift-vector = 26.405597600876234 22.1953548185108 4.493130894390984 density-guided-simulation-transformation-matrix = 0.8670686758980501 -0.2615834828985498 0.4239881988346681 0.47127429695568357 0.15472962532491696 -0.8683082863106495 0.1615315706149363 0.9526976564059948 0.2574387833509103 i’m using amber03 as a ff Thanks in advance for your help ---
**Author:** ![lmullender](https://avatars.discourse-cdn.com/v4/letter/l/8dc957/32.png) [@lmullender](https://gromacs.bioexcel.eu/u/lmullender)\ **Post date:** [July 31, 2025, 1:17pm UTC](https://gromacs.bioexcel.eu/t/unexplained-calculation-stalling-during-density-fit/12449/2 "2025-07-31T13:17:32Z")
Hi Yann, I’m not 100% sure on this but the “Rest” part of the wall time accounting doesn’t actually mean the simulation is “resting”, but it’s “the rest” of the time spent on unspecified things. You’ll notice the other named sections are all part of a regular MD simulation, but you are additionally doing density fitting, which takes a significant amount of time. I’ve never run a density fitting simulation so I can’t comment on if the specific numbers look sensible, but I would say that’s most likely what you’re seeing here. You might try switching to a 2025 version of GROMACS, because if I remember correctly, that should have added functionality for an explicit timing section for special modules (like density fitting), which should then account for most of what is now labeled “Rest”. ---
**Author:** ![YannLefrancois](https://avatars.discourse-cdn.com/v4/letter/y/dbc845/32.png) [@YannLefrancois](https://gromacs.bioexcel.eu/u/YannLefrancois)\ **Post date:** [August 25, 2025, 1:03pm UTC](https://gromacs.bioexcel.eu/t/unexplained-calculation-stalling-during-density-fit/12449/3 "2025-08-25T13:03:48Z")
Thank you for taking the time to answer me Sorry for the late answer, other stuff caught my attention. the reason I was thinking rest meant resting is my CPU and GPU usage during the simulation. ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/c86df0a0da5fa52ef4baeff357441cb5907a9a76.jpeg) neither my cpu nor my gpu seems to be computing much during the simulation which is bothering me. I dont get why.