[EMAIL PROTECTED] 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
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