[gmx-users] charge distribution

Cheong Wee Loong, Daniel dcheong at ihpc.a-star.edu.sg
Mon May 25 06:05:25 CEST 2009

Hi all,

I am using g_potential to calculate the charge distribution of my system which consists of a protein layer covalently bound to some fatty acids.  The protein layer by itself would have an overall negative charge but they system as a whole is neutral.  My question is this:  When I specify different values for the number of slices, and I sum up the charges for the protein only, I always get different results with different number of slices.  But shouldn't the overall charge of the protein layer be the same regardless of the number of slices or the size of each bin?  The difference is also quite significant so I don't think it is simply a rounding error.  For example with a 0.1 nm bin width, I get an overall charge of -3, but with a bin width of 0.05nm, the overall charge is -7.  Could someone possibly explain to me what is going on?


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