How to treat N2 molecule with a dummy atom as a rigid ball?

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1

Dear all,
In my system, there are quartz layers, and the water and N2 molecules between the quratz layers.For the N2, I used TraPPE froce field, and there is a dummy atom in the N2 molecule. I treated the dummy atom as a nomal atom with very small mass (0.000002).
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I want to treat the N2 as a rigid ball, I used fix shake commod, but cannot find clusters.
Could you please tell me how to deal with this problem?

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Many Thanks

Guohui Chen
China University of Petroleum (East China)

2

If fix shake cannot find clusters, your input is not correct (either data file or fix command). But that is irrelevant, since fix shake cannot work on linear objects with more than 2 particles, as the equations for the computing the constraint forces diverge.

You will have to use fix rigid or fix rigid/small depending on the number or n2 molecules in your system.

Axel

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