[gmx-users] protein molecule fragmenting after addition of counter ions

[Mark Abraham]

jayant james wrote:
> Hi all!
> I am attempting to counter a charge of -13 in a simulation, where the 
> protein is solvated in water.  I use the genion option and choose to 
> replace 13 solvent (water) atoms. Upon visualizing the genion output 
> structure, I find that some atoms from three of the eight cys ( a 
> Hydrogen and two sulphur atoms ) have be yanked out of the protein! I 
> wonder why this is happening!!
> Is there a way to rectify this?

It's probably a visualization artefact of some atoms being reordered at 
some point.

Mark