CG-FEP issue with Fatal error: Function type Restr. Angles does not currently support being perturbed in free energy calculations

Summary

Fatal error in restr. angle when there is no restr. term anywhere in the itp

GROMACS version

GROMACS version:    2023.5
Precision:          mixed
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support:        CUDA
NB cluster size:    8
SIMD instructions:  AVX2_256
CPU FFT library:    fftw-3.3.8-sse2-avx-avx2-avx2_128
GPU FFT library:    cuFFT
Multi-GPU FFT:      none
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      disabled
Tracing support:    disabled
C compiler:         /usr/bin/cc GNU 11.4.0
C compiler flags:   -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG
C++ compiler:       /usr/bin/c++ GNU 11.4.0
C++ compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -O3 -DNDEBUG
BLAS library:       External - detected on the system
LAPACK library:     External - detected on the system
CUDA compiler:      /usr/local/cuda-12.3/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2023 NVIDIA Corporation;Built on Wed_Nov_22_10:17:15_PST_2023;Cuda compilation tools, release 12.3, V12.3.107;Build cuda_12.3.r12.3/compiler.33567101_0
CUDA compiler flags:-std=c++17;--generate-code=arch=compute_50,code=sm_50;--generate-code=arch=compute_52,code=sm_52;--generate-code=arch=compute_60,code=sm_60;--generate-code=arch=compute_61,code=sm_61;--generate-code=arch=compute_70,code=sm_70;--generate-code=arch=compute_75,code=sm_75;--generate-code=arch=compute_80,code=sm_80;--generate-code=arch=compute_86,code=sm_86;--generate-code=arch=compute_89,code=sm_89;--generate-code=arch=compute_90,code=sm_90;-Wno-deprecated-gpu-targets;--generate-code=arch=compute_53,code=sm_53;--generate-code=arch=compute_80,code=sm_80;-use_fast_math;-Xptxas;-warn-double-usage;-Xptxas;-Werror;-D_FORCE_INLINES;-fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -O3 -DNDEBUG
CUDA driver:        12.20
CUDA runtime:       12.30

Steps to reproduce

gmx grompp -f FEP_0/em_0_FEP_Tanadet.mdp -c init.pdb -p topol.top -o FEP_0/em_0.tpr -maxwarn 5 -n index.ndx

gmx mdrun -deffnm FEP_0/em_0 -v -ntmpi 1

martini_v3.0_lipids.itp

(Please describe how we can reproduce the bug, and share all files needed - ideally both the TPR file and the raw GRO/MDP/TOP files needed to regenerate it. Bugs that only appear after running for 3 hours on 200 GPUs unfortunately tend to not get a lot of attention. You will typically get much faster attention if you have been able to narrow it down to the smallest possible input, command line, system size, etc.)

What is the current bug behavior?

Fatal error: Function type Restr. Angles does not currently support being perturbed in free energy calculations

during mdrun. grompp went fine.

What did you expect the correct behavior to be?

Jobs running normally.

Using a 8x8 pair-list setup:
  updated every 10 steps, buffer 0.060 nm, rlist 1.260 nm

Using full Lennard-Jones parameter combination matrix
There are 7 atoms and 14 charges for free energy perturbation
Removing pbc first time

NOTE: The number of threads is not equal to the number of (logical) cpus
      and the -pin option is set to auto: will not pin threads to cpus.
      This can lead to significant performance degradation.
      Consider using -pin on (and -pinoffset in case you run multiple jobs).

Initializing LINear Constraint Solver

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 116-122
-------- -------- --- Thank You --- -------- --------

The number of constraints is 1714
678 constraints are involved in constraint triangles,
will apply an additional matrix expansion of order 4 for couplings
between constraints inside triangles

Note that activating steepest-descent energy minimization via the integrator .mdp option and the command gmx mdrun may be available in a different form in a future version of GROMACS, e.g. gmx minimize and an .mdp option.
Initiating Steepest Descents
Initial vector of lambda components:[     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000     0.0000 ]

-------------------------------------------------------
Program:     gmx mdrun, version 2023.5
Source file: src/gromacs/topology/topsort.cpp (line 142)

Fatal error:
Function type Restr. Angles does not currently support being perturbed in free
energy calculations

For more information and tips for troubleshooting, please check the GROMACS
website at https://manual.gromacs.org/current/user-guide/run-time-errors.html
-------------------------------------------------------

(Please include at least the top of the GROMACS log file, as well as the end if there is any info about a possible crash. This file contains a lot of information about the hardware, software versions, libraries and compilers that help us in debugging).

Possible fixes

I don't really know - I tried to change from 10 to 2 angle type and that doesn't fix.

Edited Aug 28, 2024 by Mark Abraham