Grompp errors with v2024.3: The drift estimate should be a finite value

arfinney
Tue, 29 Oct 2024 10:56:29 +0000
User discussions

GROMACS version: 2024.3
GROMACS modification: No

Having installed the latest version of gmx, I get a grommp error on input files that work fine with previous versions:

Program:     gmx grompp, version 2024.3
Source file: src/gromacs/mdlib/calc_verletbuf.cpp (line 853)
Function:    energyDrift(gmx::ArrayRef<const VerletbufAtomtype>, const gmx_ffparams_t*, real, const pot_derivatives_t&, const pot_derivatives_t&, const pot_derivatives_t&, real, real, real, int, real)::<lambda()>

Assertion failed:
Condition: std::isfinite(drift_tot)
The drift estimate should be a finite value

I don’t believe there is an issue with the input files and I cannot spot anything in the 2024.3 release notes that relates to this error.
To check this, I installed version 2024.2 using the same cmake flags:
-DGMX_GPU=CUDA -DCMAKE_INSTALL_PREFIX=/XXX/gmx_mpi_cuda_fftw -DGMX_MPI=on -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_CUDA_COMPILER=/usr/local/cuda-12.4/bin/nvcc

grompp’ing the same input files with this earlier version works just fine. I note that mdrun and other gromacs functions work fine.

I have verified that this is not an issue with gmx_mpi by executing grompp using a serial version generated using the flags:
-DGMX_GPU=off -DCMAKE_INSTALL_PREFIX=/XXX/gmx-serial -DGMX_MPI=off

The gromacs serial executable for v 2024.3 gave the same error.

Is this a bug or has there been an update which requires changes to input files when running grompp?

My mdp file for a simulation where I am relaxing a system before a production run is as follows,

; Run parameters
integrator              = md
nsteps                  = 5000000
dt                      = 0.001
comm-mode               = linear
; Output control
nstxout                 = 100000
nstvout                 = 0
nstfout                 = 0
nstenergy               = 1000
nstlog                  = 1000
nstxout-compressed      = 10000
compressed-x-grps       = System
; Bond parameters
continuation            = no
constraint_algorithm    = lincs
constraints             = h-bonds
lincs_iter              = 1
lincs_order             = 4
; Neighborsearching
cutoff-scheme           = Verlet
ns_type                 = grid
nstlist                 = 10
rcoulomb                = 0.9
rvdw                    = 0.9
lj-pme-comb-rule        = Lorentz-Berthelot
; Electrostatics
coulombtype             = PME
pme_order               = 4
fourierspacing          = 0.10
; Temperature coupling is on
tcoupl                  = V-rescale
tc-grps                 = Water Ion Other
tau_t                   = 0.1   0.1  0.1
ref_t                   = 298   298  5
; Pressure coupling is on
pcoupl                  = Parrinello-Rahman
pcoupltype              = isotropic
tau_p                   = 1.0
ref_p                   = 1.0
compressibility         = 4.5e-5
freezegrps              = a_10
freezedim               = y y y
; Periodic boundary conditions
pbc                     = xyz
periodic_molecules      = yes
; Dispersion correction
DispCorr                = EnerPres
; Velocity generation
gen_vel                 = no

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