[gmx-users] total charge
mark.j.abraham at gmail.com
Wed Aug 28 13:36:57 CEST 2013
If you're not sure what charge your chains should have had, then you
should go back and think about the titratable residues and what you're
trying to model. Don't assume some code's defaults are what you want!
The earlier mention of "total charge -3" refers to one of the chains,
but pdb2gmx is not completely clear with its output.
On Wed, Aug 28, 2013 at 1:25 PM, Group Gro <groupgro at yahoo.com> wrote:
> Hi Dear Gromacs users,
> I have a question about the total charge of a system. I executed pdb2gmx command which the result is quited below:
> "Keeping all generated dihedrals
> Making cmap torsions...There are 7808 dihedrals, 591 impropers, 5298 angles
> 7596 pairs, 2922 bonds and 0 virtual sites
> Total mass 20072.826 a.m.u.
> Total charge -3.000 e
> Writing topology
> Including chain 1 in system: 2869 atoms 180 residues
> Including chain 2 in system: 2869 atoms 180 residues
> Including chain 3 in system: 2869 atoms 180 residues
> Now there are 8607 atoms and 540 residues
> Total mass in system 60218.478 a.m.u.
> Total charge in system -9.000 e"
> If I want to neutralize the system with Na atoms, how many atoms should I add? 3 or 9? I think I need 9 atoms, but I am not sure about that.
> Best Regards.
> S. Faraji
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