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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
