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 [image: therm.png]
<<therm.png>>
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