GROMACS version: 2024.01 GROMACS modification:No Hello! I’m working the protein-ligand complex of mdtutorials. But I face big problems about energy minimization. when I enter “gmx mdrun -v -deffnm em” this comend, there are no em.gro files in my working folder. but the three files (em.log, em.edr, em.trr) was made in my folder. and em.trr storage volume is 0kb. this is my co…

GROMACS version: 2021 GROMACS modification: Yes/No Here post your question: Hi and good day everyone. For your information, I want to split the “ligand SDF file” (CMNPD-export.sdf is the filename downloaded in my working directory) that contains a total of 413 ligands by using the command “obabel -isdf CMNPD-export.sdf -osdf -O *.sdf - -split” after I have downloaded the li…

Hi All, My system contains 60 polymers and I want to calculate the average end-to-end distance change with time. In the index file if I define indexes of the starting end and the ending end of the polymer with the following command would it give me the average end-to-end distance with time? gmx polystat -s …/…/…/run.tpr -f run0-14_nopbc.xtc -o 0.xvg -n index.ndx My index file lo…