[gmx-users] Protein preparation

[Quin K]

Hi

I'm new to Gromacs.
I have a question regarding protein preparation for MD simulation.

I ran a 50 ns MD simulation but later found out that the protein has a
charge.
I found that there is a Mg2+ Ion in the protein crystal structure. Should I
remove this Mg2+ ion from protein before addition of ions to the protein ??

Following is the protein I used.

http://www.rcsb.org/pdb/explore.do?structureId=3a5j

Thanks
Regards!
Quin.