[gmx-users] simulating a protein homodimer

[Justin A. Lemkul]

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
> 

-- 
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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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