May I ask why you need the system to be net neutral *in vacuum*? Notice that I stress "in vacuum". I mean, it's not like you need to use PME or anything like that. Vacuum simulations are usually done without PBC, so a simple Coulomb potential without cutoff should be fine.
I don't routinely perform vacuum simulations, so I may be wrong. Correct me otherwise. Best regards, João On Tue, Sep 1, 2015 at 11:57 AM, tasneem kausar <[email protected]> wrote: > Dear Gromacs users > > I am trying to neutralized the protein having two chains with four negative > charge. > I ran the command line as : pdb2gmx -c prtn.pdb -p -o -glu -asp. > I have chosen one protonated glu and one protonated asp for each protein > chain. > The net charge is now zero. > Am I going through the right step for the neutralization? > If there is any other way to neutralize protein, please suggest. > > Thanks in advance > -- > 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 [email protected]. > -- 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 [email protected].
