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GROMACS modification: Yes/No
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There is mentioned that if gen pairs is set to no that means get 1-4 parameters from pair type list, and if it is set to yes then it will generate from normal LJ parameter using fudge LJ.
But my question is that I am working with small organic molecules where I don’t want to consider any non bonded interaction. So what I have to set in gen pairs and nrexcel.
nrexcel is used to excluding non bonded interaction between atom after a certain no of bond. So for pentane I have to set nrexcel= 4 if I don’t want to consider non bonded interaction.
I set gen pairs no and nrexcel=3 randomly and didn’t provide any pair list in itp file, is it alright or I am doing something wrong. Please suggest me.