[gmx-users] excess use of suplhate ions

[Justin Lemkul]

On 9/24/12 3:01 AM, Arunima Kumar wrote:
> Dear Sir
>
>           I have performed MD simulation of a protein and the system uses  2
> sodium and 19256 SO42   as charge neutralization system. I am unable to
> understand why my protein uses this much of negative ions. Negative ions
> used in such a high quantity might genertae a highly negative system.
> Should i proceed further or check my protein in terms of amino acids before
> proceeding to next step.
>

It seems highly unlikely to me that any protein has a net charge of nearly 
+40000.  I would check carefully before proceeding.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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