Hi I use the gromacs package (2016) for simulate polarized water and ions.
When I try to use the h2order for water orientation I get wrong results (file attach). I use the make_ndx to create a index file with the atoms OH2 H1 H2 only.
Is there a correct way to calculate the water orientation?
Kind regards
Jun Zhou
Hi Gonzalo,
Hope this can still help you.
Since you are using the four-point water model, the negative charge has been assigned to the virtual point, you need to make a selection as an order "MW HW1 HW2". Then you can get a good result.
To achieve this, maybe you can use "gmx select", and then input "name MW HW1 HW2 permute 2 3 1" to rearrange the order of the selection.
Please correct me if I am wrong, thanks.
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