[gmx-users] special coulombic interaction in 1-3 atoms (bonded atoms)

Ting Zheng zhengting.yq at gmail.com
Thu Feb 12 00:09:07 CET 2015

Hi all,
I have a problem that puzzle me a long time.
In my system I define a angle and two bonds between 2-1-3 and 2-1, 2-3
atoms. Generally the coulomb and LJ interaction between 1-3, 1-2, 2-3 atoms
was excluded. However, in my position, the potential parameters for these
three atoms is quite abnormal since the interaction (only coulombic
interactions) in 1-3 atoms was still existed which means I have add this
special interaction into my non-bonded list.
So my question is that how should I add this special interactions? I am
using Amber force field. It seems that the [pairs] items in the top file
can make this special interaction come true. But It seems that additional
interaction in 1-4 atom could be added via using the [pairs] items. But I
am not quite about this. Is there anyone who can do me a favor about this
Secondly, how should I use only coulomb interactions in my system?

Thanks very much

Best Regards

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