GROMACS version: 2024 GROMACS modification: Yes/No Hi, I follow all the necessary steps in building GROMACS with CP2K, no error arise in all of the steps, however whenever I try to use it, GROMACS can’t read the QM/MM parameters in my mdp file. this is my cmake parameters: cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=on -DBUILD_SHARED_LIBS=OFF -DGMXAPI=OFF -DGMX_INSTALL_NBLI…

GROMACS version:2021.7 and 2023.4 GROMACS modification: No Here post your question Dear all， When I simulated a large water system (100000 water molecules) using the TIP5P water model, it was vaporized at 273K and 1bar. The initial structure was built using ‘gmx solvate’, followed by an energy minimization. Using the same procedure for smaller systems (10000 water molecules), I…

Hi, I built a 4 * 4 * 4 box and wanted to add an electric field along the Z axis. What I understand from the"Electric-field-z = -0.01 0 0 0" in the MDP file is that this is the electric field from the bottom of the box to the top of the box. I would like to ask my understanding is correct? Thank you. 1 post - 1 participant Read full topic

GROMACS version: 2023.3 GROMACS modification: No I have come across posts that help with restarting without a cpt file (although I am still confused), but I wanted to check if it was okay to do so in my case, or if I should just start from the beginning again (although this simulation had already run for 18 days). I am using a HPC with a slurm manager which paused my sbatch mdru…

Hi I tried running cmake command to get compiled gromacs GPU but I get the following error vboxuser@mbox:~/Downloads/gromacs-2024.1/build$ cmake --version cmake version 3.29.0 CMake suite maintained and supported by Kitware (kitware.com/cmake). vboxuser@mbox:~/Downloads/gromacs-2024.1/build$ cmake … -DGMX_GPU=CUDA -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/marydoe/programs – T…