[gmx-users] (no subject)

[Mark Abraham]

chris.neale at utoronto.ca wrote:

>>2..when i'm trying to run grompp
>>  Note: System has non-zero total charge : -6.000002e+00.
>>  is it necessary to neutralise the charge, if so genion 
>>  has to run Na means how much i've to add..ie how to calculate it...
> 
> 
> You must have a charge neutral system to use Ewald/PME/etc... 

That's not true. There's nothing intrinsic about those treatments that 
prevents non-neutral systems... quite the contrary in fact, although 
I've seen this "must-be-neutral" view expressed on this list before. 
Further there is nothing in the gromacs 3.3 manual that suggests there 
is a gromacs constraint to have neutral systems, although I haven't ever 
wanted to try it out myself to see. Whether you'd want a non-neutral 
system for a given problem is a matter for the user to decide :-)

Mark