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