GROMACS version: 2019.4
GROMACS modification: No
Here post your question
I met the segmentation fault when I tried to run “gmx mdrun” command.
I tried to reproduce the umbrella sampling from a tutorial page http://www.mdtutorials.com/gmx/umbrella/index.html but with my own structures. However, I met segmentation fault at step 4 but the tutorial structure looks good. I don’t know what is the problem with my own input.
It seems this forum cannot upload the PDB file?
I found the error comes from the N terminal residue. After I delete this residue the program runs successfully. Could anyone explain what is the problem of this residue?
ATOM 1 N THR A 1 240.241 67.891 -69.279 1.00 N
ATOM 2 CA THR A 1 238.975 67.691 -69.975 1.00 C
ATOM 3 C THR A 1 239.165 67.728 -71.523 1.00 C
ATOM 4 O THR A 1 238.703 67.053 -72.261 1.00 O
ATOM 5 CB THR A 1 237.933 68.749 -69.566 1.00 C
ATOM 6 HG1 THR A 1 239.140 70.183 -69.431 1.00 H
ATOM 7 OG1 THR A 1 238.438 70.058 -69.856 1.00 O
ATOM 8 CG2 THR A 1 237.639 68.659 -68.077 1.00 C
Just as a guess, atom names might be in the wrong order, leading to mixed up coordinates for atoms that might blow up your system - did you check all output of grompp and pdb2gmx?