Effect of using Na or K for MD Simulations

Dear All,

I am working on a Protein-DNA complex. I run my simulations with Amber14sb-PARMbsc1 force field. We performed couple of simulations to see the difference of using different ions (e.g. Na and K). As can be seen in the figure, we observed an explicit difference between the potential energy values โ€‹โ€‹of simulations containing Na and K, regardless of random seed. Do you have any idea why and what could lead us to? Thanks in advance.

  1. Na is different from K in vdw interactions. This will directly result in a difference in potential energy.
  2. The two types of ions will have different interactions with DNA, which will give again different energy values.
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