GROMACS version:2021.5 GROMACS modification: No Sorry for my poor English. Please lend me your help, everyone. I have three questions for you. ①I would like to use the “AMBER” force field to flow the structure of the covalent linkage between sugar and protein with “GROMACS”. I’m thinking of using “CHARMM-GUI”, but what are the bonds, angles, and torsions that contain covalentl…

GROMACS version: 2022.3, 2022.5, 2023.1 GROMACS modification: No Hello, I’ve been having issues, trying all three of these GROMACS distributions. I’m running on an HPC, and I have included the basic error logs for the outputs of cmake and make check for the blank run after logging into the HPC. After gcc-7.5.0 fails, I install gcc-10/g+±10 and try the installation once more with …

GROMACS version:2022.5-Colvars_2023_05_01 GROMACS modification: Yes I am attempting to use ABF in the colvars module for my simulation. I have tried installing several versions of Gromacs (gromacs2021.6-colvars, fresh download of gromacs2022.5 that I patched with colvars). I have tried installing them on my own laptop in Ubuntu22.04 on WSL2 as well as in a folder I have write per…

GROMACS version: 2022.4 GROMACS modification: Yes (Colvars module) Hi all, I have been trying to model an sII THF hydrate in GROMACS 2022.4 for about a month now. My starting structure is a hydrate determined from x-ray crystallography, with THF molecules added manually to large cages found in the hydrate. When I perform an energy minimization on my starting structure, I consis…