[gmx-users] total charge
groupgro at yahoo.com
Wed Aug 28 13:25:33 CEST 2013
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
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.
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