[gmx-users] basic question for a MD run

jean-marc vuissoz vuissozjm at bluewin.ch
Fri Aug 8 21:33:00 CEST 2003


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

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