[gmx-users] [quick question on workshop and membrane]
science at louic.nl
Fri Sep 23 11:37:09 CEST 2005
spitaleri.andrea at hsr.it wrote:
> 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 don't know about md workshops, but if there are any, I am also
interested. Some tutorials for membrane proteins are available on the
internet. This is one that helped me to start with gromacs:
> 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?
This is no problem, it's just a rounding error. The answer has been
previously posted on this list, which can be searched from the GROMACS
> Any suggestion are very welcome,
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