[gmx-users] about counterions
Mark.Abraham at anu.edu.au
Mon May 14 16:10:01 CEST 2007
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.
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