GROMACS version:2020.6
GROMACS modification: No
Here post your question :
Hello everyone,
I’m attempting to generate a topology file using Gromacs with the Drude force field, but I’ve encountered a critical issue. The error message I’m receiving is as follows:
Fatal error:
In the .rtp file in residue anisotropic_polarization at line:
DBR6 BR6 C6 C1 C5 1.80000000 0.60000000 0.6000000
Does anyone have a solution for resolving this problem?
thank you
You cannot use version 2020.6. None of the GROMACS official releases support Drude. Only the Drude branch of the the git repository has those features. I will warn you that at present it is not production-quality code and should not be used for science you intend to publish.
I appreciate your response greatly.
Are you familiar with any polarizable force fields compatible with GROMACS?
best regards.
Only trivial shell-type models that are quite old. GROMACS supports some basic features but they aren’t often used.
Sir, I have used the Drude branch of the git repository. I am receiving the same error.
Fatal error:
in .rtp file in residue anisotropic_polarization at line:
DBR6 BR6 C6 C1 C5 1.80000000 0.60000000 0.60000000
Can you please guide me ?
What is the output of gmx version?
You need to switch to the Drude branch of the git repository and install that code. 2025-dev does not include Drude features, because they have not been merged into the main branch.
Sir,
Thank you so much for your response.
I will download from Drude branch of the git repository.
Just to be sure, this is the link for the code in drude branch.
Yes, but you can switch to that branch easily from what you already have in the main git repo with git checkout drude.
cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_FLAGS=“-O3” -DCMAKE_CXX_FLAGS=“-O3” -DGMX_MPI=ON -DGMX_GPU=CUDA -DGMX_SIMD=AVX2_256 -DCMAKE_INSTALL_PREFIX=/path was provided -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Debug -DBUILD_SHARED_LIBS=off -DGMX_EXTERNAL_LAPACK=OFF
sed -i ‘s/GMX_BUILD_OWN_FFTW_URL:STRING=.*/GMX_BUILD_OWN_FFTW_URL:STRING=/path was provided where fftw.tar.gz file was saved’ CMakeCache.txt
make
[ERROR]
CMake Error at fftwBuild-stamp/verify-fftwBuild.cmake:29 (message):
error: MD5 hash of
Sir,
While installing I faced issue with fftw path. The above commands works for my other installation of GROMACS and 2025-dev gmx version. Iam not able to fix this issue.
Path >> gromacs-drude/src/contrib/fftw/ This path have a file name “fftw-download.cmake.cmakein”
message(STATUS “downloading…
src=‘@remote_url@’
dest=‘@local_path@’”)
file(DOWNLOAD “@remote_url@” “@local_path@”
SHOW_PROGRESS STATUS status LOG log)
list(GET status 0 status_code)
list(GET status 1 status_string)
if (NOT status_code EQUAL 0)
message(FATAL_ERROR “error: downloading ‘@remote_url@’ failed
status_code: {status_code}
status_string: {status_string}
log: ${log}”)
endif()
message(STATUS “downloading… done”)
Do I need to make any changes in this file.
Kindly please guide me through this.
Ok Sir.
Sir,
While installing I faced issue with fftw path. The above commands works for my other installation of GROMACS and 2025-dev gmx version. Iam not able to fix this issue.
Kindly please guide me through this.
I have no idea what that aspect of the build system is. Your command is not valid as written, because you are simultaneously telling cmake to build FFTW but then you are providing the location of an existing FFTW installation with -DCMAKE_PREFIX_PATH. The two options are mutually exclusive. You should be able to install the software with a much simpler command. Most of those options are unnecessary. Do not install in debug mode; it will be horrifically slow.
Ok Sir.
Thank you sir for your response.
I will try with simpler commands.
