[gmx-users] charged systems

Elisabetta Gianazza Elisabetta.Gianazza at unimi.it
Wed May 22 08:49:23 CEST 2002

Dear all,
I set up a system (Protein + water) for MD with total charge -8. I read 
all the related mail in user-list archives about non-zero charged 
systems and I am not sure to have understood everything.

The charge of my system is high, so I need to add 8 Na to neutralize it. 
Is it correct if I put ions with genion, according to the most favorable 
electrostatic potential (not at random)?

Should the ion insertion precede the EM step?

How should I treat long range electrostatics? I read cut-off is not 
suitable with ions (high risk of artifacts); is PME with the  parameters 
below adequate for EM and then 2-3 ns MD?
coulombtype = PME
rvdw = 0.9
rlist = 0.9
rcoulomb = 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5

In a system with zero total charge (isoionic protein)  and no ions, may 
I use cuts-off instead of PME?


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