[gmx-users] planar geometry: dummy atoms or angle restraints?

Rebeca García Fandiño regafan at hotmail.com
Fri Oct 2 18:32:43 CEST 2009

I am trying to simulate an organic system which has a planar-square Pt center. To mantain the planar geometry of the metal, I have thought about 2 possibilities:

-introduce 2 dummy atoms at the axial possitions of the metal; however, I get errors complaining about these extra atoms has mass 0. 
I have read the manual and also looked at the GMX list, and I have found that other people have also found problems of these type. I have read that in case such as acetonitrile the advice was to redistribute the mass over N and CH3 such that centre of mass is unchanged and inertia tensor is not modified too much either. Should I do something similar in my case? Which mass should I redistribute? The mass of the whole molecule? 

-increase the harmonic restraints for angles where the metal is involved. Would this approximation would be as correct as the one mentioned before or would it better to use dummy atoms?
Thank you very much for your help in advance.
Best wishes,
Dr. Rebeca Garcia
Universidad de A Coruña
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