Stephen Edgcomb wrote:
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.
Energy minimization should not result in any large-scale movement of the
protein. Sounds like a classic case of PBC:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-Justin
Any help would be appreciated, and please let me know if more
information is required to answer my question.
Thank you,
Steve
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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