[gmx-users] charge neutralization in vacuum simulations

João Henriques joao.henriques.32353 at gmail.com
Tue Sep 1 12:08:07 CEST 2015

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

Best regards,

On Tue, Sep 1, 2015 at 11:57 AM, tasneem kausar <tasneemkausar12 at gmail.com>

> 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
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