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.
Mark
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