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

Mark Abraham mark.j.abraham at gmail.com
Thu Feb 12 00:15:56 CET 2015

On Thu, Feb 12, 2015 at 12:09 AM, Ting Zheng <zhengting.yq at gmail.com> wrote:

> 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
> problem?

[pairs] are used to add modified 1-4 interactions, but in principle can be
used to add anything, such as 1-3 in your case.

> Secondly, how should I use only coulomb interactions in my system?

Set VDW parameters to zero, mdrun will gleefully take advantage of that!


> Thanks very much
> Best Regards
> Ting
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