[gmx-users] exclusions indices

[xieyh at hkusua.hku.hk]

Dear users:

In my system, 2 molecules and solvent (protein DNA SOL) are contained. Now, I
expect to exclude the nonbonded interactions between e.g. atoms 1, 2 ,3 4 in
DNA and all the atoms in SOL. 

Normally, I can realize it by defining a [ exclusions ] section. But in my case,
the number for SOL is huge, so it is almost impossible to explicitly write each
SOL atom number while defining [ exclusions ]. Can you suggest any simple one,
it has better be like:

[ exclusions ]
1   atom index in SOL(e.g. 100, 101, 102, .....9999,10000)
2   atom index in SOL(e.g. 100, 101, 102, .....9999,10000)
3   atom index in SOL(e.g. 100, 101, 102, .....9999,10000)
4   atom index in SOL(e.g. 100, 101, 102, .....9999,10000)

I think GMX can do it, but how?


Thanks and regards,
Xie YH 
Hong Kong Univ.