[gmx-users] Dimer simulation

[Kavyashree M]

Dear users,

I was trying to simulate a protein dimer covalently bond with
a disulphide bond (230+230 aa long). I used usual protocol
as used for simulation of a monomeric protein, using gromacs-
4.5.3, dodecahedron box, tip4p water model and protein to
box distance of 1 (-d in editconf). In the middle of the simulation
when i checked for minimum image violation there was huge
clashes. I am extremely sorry I have been asking regarding this
many times but in this it is a dimer and I am not sure what mistake
I have done because this happened while simulating another dimer
also though not sever. Hence I seek some guidance from this
community regarding the problem. I attach the graph herewith.
Kindly help. Let me know if I need to give any other information.

Thanking you
With Regards
M. Kavyashree
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