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1 vote

Visualising the spatial distribution of water structure using VMD

VIAMD software will allow you to do that. You can use the sdf function in the script editor after loading your trajectory. It would like something like that depending on your topology: ...
mathieu linares's user avatar
3 votes

Exclusion of Lennard-Jones potential between O-H and H-H in water models

The original publications may give some reason for omitting HH and OH Lennard-Jones terms -- but my first assumption would certainly be computational simplicity. Having said that, these models are ...
Shern Ren Tee's user avatar

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