[gmx-users] How to control 1-5 interaction

Makoto Yoneya yoneya at nanolc.jst.go.jp
Thu Mar 18 08:24:01 CET 2004

Dear GROMACS users:

I'd like to know the proper way to control 1-5 interaction within molecule.
The 1-5 interaction which I'd like to control is as following.

          /        \
        CH3      C----
      atom i     ||
               atom j

Between the branched CH3 (i) and the carbonyl O (j) , there is rather strong
interaction even that is 1-5 distance.
A possible way will be as follows.

[ exclusions ]
  i    j
  j    i
[ pairs ]
  i    j     1    0.****E-02   0.****E-05  ; control this interaction

Is this correct way to control the 1-5 interaction?
Are there more adequate way?

Thank you for advance.

Makoto Yoneya Dr.
Yokoyama Nano-structured LC Project
Tsukuba, Japan

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