[gmx-users] protein molecule fragmenting after addition of counter ions
Mark.Abraham at anu.edu.au
Fri Jun 6 01:26:43 CEST 2008
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
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