[gmx-users] Max #atoms in a charge group: 68 > 64

[Mark Abraham]

Samuel Coulbourn Flores 花山 wrote:
> So, is it generating the charge groups based on residue numbering?

I said to look at your .itp/.top file... below you've pasted your .pdb 
file. I can't tell what your charge groups look like...

>  Can 
> I solve the problem by just editing the residue number column such that 
> the ligand is now composed of two "residues"?  If not, how should I 
> specify how the molecule is to be broken up into charge groups?  How 
> strict is the requirement that the charge be an integer?  It seems 
> unlikely that any subset of the molecule will have net integer charge.

That all depends how you generated the topology in the first place.

Non-integral charge-groups with group-based cut-offs will make strict 
energy conservation difficult/impossible, though whether that has much 
effect depends on other stuff. I've no idea if this 64-atom limit is 
just a weird genion thing, or a problem you'll see with mdrun too...

Mark