[gmx-users] Protein Chains Spatially Separated After Energy Minimization

[Justin A. Lemkul]

Benjamin Er wrote:
> Hello Everybody,
> 
> I have 2 different protein chains (not a homodimer), chain C and chain F 
> in a PDB file.
> These 2 proteins are interacting proteins close in proximity.
> I would like to use energy minimization (EM) and equilibration (EQ) to 
> approximate the most relaxed interacting conformation between these 2 
> proteins.
> However, after EM, these 2 chains become far apart in space. (I checked 
> with PyMOL using editconf for the resulting EM .gro file)
> My previous EM and EQ run for a different set of 2 proteins did not have 
> this error.
> May I please know how I can rectify this?
> 

This sounds like a normal consequence of PBC.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

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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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