Hello All I am trying to simulate a protein homodimer.
My command lines are: pdb2gmx -f dimer.pdb -p dimer.top -o dimer.gro -ignh -ter -chainsep interactive grompp -f minim.mdp -c dimer.gro -p dimer.top -o input.tpr mdrun -nice 0 -v -s input.tpr -o minim_traj.trr -c minimized.gro -e minim_ener.edr editconf -f minimized.gro -o mdrundimer.pdb the mdrun step results in the second chain of the dimer translocated away from the first chain. I do not know what is causing the translocation. The dimer should just be completing a gas phase equilibration. Any help would be appreciated, and please let me know if more information is required to answer my question. Thank you, Steve
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