[gmx-users] nrexcl 3 or 4 in combination with pairs 1-4

[Claus Valka]

Dear Gromacs users,

my system has both 1-4 and 1-5 interactions. I list
all of them in pairs. According to nrexcl definition
(gmx mail list), "setting nrexcl to 3 or 4 does NOT
remove LJ-14". Yet, by switching this option from 3 to
4 I have a lot of differences not only in the non
bonded but also in bonded interactions as well. 
Searching further the forums I came accross :
Priority of [ pairs ] and nrexcl?, yet it is
unanswered. 

Question1:
If I have both pairs 1-4 and nrexcl 3 that means that
atoms, three bonds away, have non-bonded AND LJ14
interaction or ONLY LJ14 interaction?

Question2:
In pairs should I declare the atom indexes only once?
For example i j is is enough for declaring the 1-4
interaction between i and j or have I to insert also j
i? Doing so I get different results.

Thank you,
Nikos
 




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