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

[Louic Vermeer]

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.
 > First:
 > 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:
http://www.dddc.ac.cn/embo04/practicals/9_16.htm

 > Second:
 > 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 
website.

 > Any suggestion are very welcome,
 > thanks
 >
 > Regards
 > andrea


Have fun!
Louic Vermeer