[gmx-users] basic question for a MD run

[jean-marc vuissoz]

hello,

here are some basic question :
a) when I put periodic conditions, does I have to have a neutral charge 
for my system (ie probably putting some ion in the system) ? is there a 
easy way to check the charge of your system once you have it ?

b) I try to equilibrate a system ( a protein with a ligan (also 
protein) in a water box), what type of pressure condition should I put, 
I try with berendsen but after 1.4ns I get an rmsd of the Calpha which 
is between 0.5-0.6 nm (not very good for an equilibration )

best thanks

vuissoz jean-marc