[gmx-users] simulating a protein homodimer

[Stephen Edgcomb]

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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