[gmx-users] PME question, again

Erik Lindahl lindahl at stanford.edu
Wed Jun 19 19:01:55 CEST 2002

Ivano Eberini wrote:
> Dear Erik,
> I run 1 ns molecular dynamics of a protein in water with PME. To obtain 
> a neutral system, I put 8 Na ions in the box. One of them moved across 
> the box boundary during dynamics. Should I rerun MD with a wider box? I 
> usually try to minimize the box dimensions to reduce the computing time. 
> Is there any way to evaluate the effect of this ion moving across the 
> box upon the MD?

Well, it won't have any effect on the interactions; you do get exact 
forces and energies in the approximation of an infinite system of 
replicated boxes. It's just that the concept of having a charge flow in 
an infinite system is a little strange theoretically, and if you for 
instance plot the net dipole of your box you might see that...

I wouldn't worry about it, nobody else does :-)



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