[gmx-users] about counterions

[Mark Abraham]

Rui Li wrote:
> Dear all,
> I am new to gmx.
> When I run grompp, it prompt:
> System has non-zero total charge: 1.172000e+01
> 
> The number isn't integer, So how many counterions I should add?

Never mind about ions, probably your topology is broken before you got 
started :-) Check your capping groups. If you used pdb2gmx, have a look 
at the right hand (comment) column of the atom listing, where it shows 
the cumulative charge. This will help you find the residue where things 
start getting non-integral.

Mark