[gmx-users] genion question

Mark Abraham Mark.Abraham at anu.edu.au
Tue Aug 25 23:53:08 CEST 2009

Paymon Pirzadeh wrote:
> Can I change the charge of Na ion added from +1 to +0.99 to cancel the
> negative charge exactly? Does that hurt science or simulation?

It's probably irrelevant. The representation of "decimal" numbers on 
computers can be inexact, such that things like 0.02 added to itself 100 
times does not pass a test for equality with 2. You may be observing 
this kind of thing here. Your protein's [atoms] directive has a running 
count of the total  charge on the molecule - go and read it and see that 
each residue has an integral charge. Hopefully you can observe where the 
rounding error might be occurring and you can make a judgement about 
whether this might be true.


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