[gmx-users] some problems by freshman

[zpxu]

Dear All:
    I am wondering if you can show me such fundamental things:
1) I want L-J interaction only between the C_I(innertube) and C_O(outertube)
atoms (two type of atoms in one molecule).
    and their are four sections concern L-J potential.
    a)section [atomtypes] in topology file
    b)section [nonbond_params] in topology file
    c)section [pairtypes] in topology file
    d)section [pairs] in topology file
    now I only use b).
    is it ok?
2) the unit of potential parameters, I use nm,kJ/mol
    is it ok?
3) my coordinate is at nanometer scale, so I shift it by 3nm, let the tubes
in box.
    
4) I set charge to zero, and set charge group arbitrarily.will it be ok?


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