GROMACS version: 2021.4 GROMACS modification: No Hello, I want to simulate the flow of water molecules through a nanopore under a pressure drop. To apply the pressure drop, I would like to use the same technique as the one used in this paper or this one. This one consists in applying an external force f to all the oxygen atoms contained in a slice of the tank such that \Delta…

Brief description of tools/files: Python interface Link: GromPy (Rene Pool) · GitHub Contact person (name and email address): Rene Pool How the work has been tested/reviewed: see publication 1 post - 1 participant Read full topic

GROMACS version: 2019.2 GROMACS modification: Yes, patched with PLUMED 2.5.2 Hi everyone, I would like to perform REST2 simulations in GROMACS. I already installed gromacs 2019.2 version patched with plumed 2.5.2. I have provided the cmake commands for the reference. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=CUDA -DGMX_MPI=on -DGMX_USE_RDTSCP=ON -DGMX_SIMD=AVX2_128 -DREGRESSIONTEST_DOW…

GROMACS version: 2021.4 GROMACS modification: /No Hi all, I’m trying to simulate a myeloperoxidase protein monomer in water at ambient conditions, but I’m continuing to run into an problem that I don’t know how to solve. I’ve taken the crystal structure (3F9P) from RCSB and parameterized the metal-containing center using MCPB.py, but I’m unable to energy minimize my structure. S…