my system comprises of calcium depleted protein in spc water and i added sodium ions to neutralize the protein (as calcium were depleted so many sodium ions were needed) but after simulating in gromacs i found that sodium ions diffused into my protein (as visualized in vmd). what can be the problem?
please guide!!
Probably because the protein contain so many negatively-charged residue like aspartate or glutamate.
Well in my opinion it is only natural that natrium ion is tend to get close to the aspartate or glutamate resude all the time (http://www.ks.uiuc.edu/Research/kvchannel/). There are even water molecule that binding tightly in certain region of protein, it is a common thing.
Even small molecule like enzyme inhibitor could rarely leave the enzyme thanks to the electrostatic funneling near the binding site:
http://www.ks.uiuc.edu/Research/influenza/
Check the Elucidating a Drug Binding Funnel part.
Alright, what about the ratio between the size of your protein and your system size? If your system size is only around +2 times the electrostatic cutoff from the surface of the protein then it is very more likely that the ion will get attracted to the protein and trapped inside of it.
For example, if your electrostatic cutoff is 12 Angstrom (1,2 nm), and your protein is 50 Angstrom, then 50 + (2 * 12) Angstrom = 74 Angstrom (7,4 nm). So having a system of a size 74 Angstrom when your protein is 50 Angstrom and electrostatic cutoff around 12 Angstrom will more likely to give you such result. Perhaps enlarging the system box will help solve this problem.
The other solution would be to add the solvent in stepwise. First add solvent in a box a bit further than protein, and replace some of the solvent with the sodium/chloride ion, then solvate again the entire box. But this will be slightly cheating and unnatural.
Diameter? Why is there a diameter and x * y * z size? But I think such system would be sufficient for protein with size around 60 kDa which correspond to around 7 * 5 * 5 nm.
If you want to measure the size of your protein then perhaps the quickest way would be to measure the distance between two atom with the longest distance within protein. In VMD it can be easily done by choosing bond mode and click the two atom that wanna be measured. I usually use simple command that could measure the minimum and maximal x y z of a protein.
Well, I'll return to my first opinion then. Just let it be, and check how common it is via literature research :)
http://scholar.google.com/scholar?q=sodium+molecular+dynamics+aspartate+glutamate&btnG=&hl=en&as_sdt=0%2C5&as_vis=1
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