[gmx-users] Again: Non-integer charges in tpr-files

Marc Saric marc.saric at mpi-dortmund.mpg.de
Thu Oct 3 20:03:33 CEST 2002

Erik Lindahl wrote:

> Sorry, perhaps I misunderstood you; if you expected a net charge of 24 
> in the system, this is perfectly OK.

That was probably me, who tends to be a bit fuzzy in explaining things...

> I actually tried to "fix" this a long time ago, but it isn't trivial; we
> are summing a lot of charges, and due to the way they are represented in
> hardware they aren't exact. One option would of course be to only warn
> when the net charge is more than 0.01% of the system charge RMSD or 
> something, but that might hide things like having one charged lipid 
> among 1024 uncharged ones... I'll see if we attack it again.

Maybe adding a sentence like this somewhere (probably after the warning 
and a somewhat longer explanation with some sort of decision-tree in the 
manual) might suffice in most cases?

Might spare you a lot of programming! ;-)

Thanks again for the help.

Bye,  Marc Saric

Max-Planck-Institut fuer molekulare Physiologie
Otto-Hahn-Str.11  44227 Dortmund  phone:0231/133-2168

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