[gmx-users] [quick question on workshop and membrane]

spitaleri.andrea at hsr.it spitaleri.andrea at hsr.it
Fri Sep 23 11:03:06 CEST 2005

Apologies if you get this email twice (problem with the server):

Hi there,
this is my first queries on the mailing list.
is there any planned workshop on molecular dynamics/bionformatic?
I am running gromacs on protein-membrane interaction. The steps for the
MD are:
em for the protein in water -> lie the protein on the membrane and run
em and then md.
grompp leads to a warning about system charged +5. I use genion to
neutralise them (considering the solvent in the option) but
it yields to the system charged +2.5e-5, very small but still charged.
Is it normal? Do you suggest to neutralise first the protein and then
add it to the membrane?
Any suggestion are very welcome,


Andrea Spitaleri 
Dulbecco Telethon Institute 
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)

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