Hi,
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
Spain
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