GROMACS version:2024.1 GROMACS modification: No Hi all, I’m following the tutorial on Protein Ligand Complex by Dr. Lemkul and I encountered a problem with restraining the ligand. Protein-Ligand Complex I followed the instructions and first restrained the H atoms on JZ4. Then I added restrain infomation at the end of topology file. I then grouped protein with ligand. Protein_JZ…

Hi everyone! I am trying to simulate a crystal structure (PDB) which comes with N-linked glycosylation (N-acetylglucosamine). Each N-acetylglucosamine is further linked with different sugar molecules like mannopyranose so each glycosylation exists as a chain with a few additional molecules . Which force field shall i use? I am thinking to try with ff Gromos 54a7 but i think in th…

GROMACS version: GROMACS modification: Yes/No Here post your question I have simulated 1 microseconds of a protein and now I wold like to extend it. This is how I did simulation: First, in the md.mdp file I set nsteps to 50000000 and dt 0.002 picosendos (simulating 100 nanoseconds in each run). Then I wrote the code to execute mdrun for 100 nanoseconds. When the 100ns was compl…