Unexplained calculation stalling during density fit

YannLefrancois
Mon, 28 Jul 2025 12:33:23 +0000
User discussions

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

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

3 posts - 2 participants