GROMACS version: 2024.1 GROMACS modification: Yes/No Here post your question I am compiling the CHAP program on WSL2 (Ubuntu). It requires gromcs to be installed. I have gromacs installed and available in the terminal. However, when executing make command, I encountered the following error- In file included from /mnt/d/Simulation/chap-version_0_9_1/src/aggregation/boltzmann_ene…

GROMACS version: 2022.5 GROMACS modification: no I am doing the steered md now. How can I make a pull.tpr file? What commands should I enter? 1 post - 1 participant Read full topic

GROMACS version: 2024.1 GROMACS modification: No System Information: Operating System: Ubuntu 22.04 CUDA Version: CUDA 12.4 GPU Driver Version: 550.54.15 GPU : NVIDIA GeForce RTX 4090 CPU : 13th Gen Intel(R) Core™ i9-13900K This my cmake command cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DGMX_DOUBLE=off After I completed the compilation, I …

GROMACS version: GROMACS modification: Yes/No Here post your question Hello, I have a small system containing 134 molecules of water. I managed to run some simulations on it without problems. However, now, for some reason, the simulation runs very slowly. The .mdp file is: ; Run control integrator = sd ; Langevin dynamics tinit = 0 dt…

GROMACS version: 2022 GROMACS modification: Yes/No Here post your question: Dear reader, I have been trying to pass through the topology generation step for my protein, for which one residue (Thr) has been phosphorylated. After following a lot of forums, websites and the gromacs manual itself, I edited all the possible residue topology files, starting with aminoacids.rtp. When …

GROMACS version: GROMACS modification: No What is the epsilon parameter unit in the LJ force-field file oplsaa (ffnonbonded.itp). In the main paper, its unit is KCal/mol but the Gromacs standard unit is KJ/mol. Was this unit changed in the force field file or is it internally changed by the Gromacs during the run? 1 post - 1 participant Read full topic

GROMACS version: 2023.4 GROMACS modification: No Hi everyone, I am new to GROMACS and I have been following the Lysozyme in Water tutorial to simulate my docked protein-protein complex generated from ClusPro to check for the structural stability and flexibility of the docked complex. However, after running a 120ns simulation, my RMSD plot for my complex does not show that the doc…

GROMACS version: 2023.2 GROMACS modification: No Here post your question Hi, I am trying to build gromacs with spack ( spack install gromacs%nvhpc +mpi +cuda cuda_arch={cuda_arch} +cufftmp) and I have tried nvhpc 23.5 and 24.3 versions and it didn’t build. I am getting the following error message during the build stage : ==> Installing gromacs-2023.2-egcf5t2p57er6f3ix6ihkxt…

GROMACS version:2024.1 GROMACS modification: No I am running a simulation on a protein that requires a cation and coordinating water molecules to be bound. For reference I am using the charmm36-July2022 forcefield and had the water molecules identified as TIP3P. During the pdb2gmx step, when i attempt to input a coordinate file that has my protein, 2 ions and 4 water molecules wi…