[gmx-users] dummy atoms in planar square Pt

Rebeca García Fandiño regafan at hotmail.com
Thu Sep 24 19:20:46 CEST 2009


I am trying to simulate an organic system which has a planar-square Pt center. I am following the methodology employed in JACS 2008, 10040 (where they use amber calculations). There, they use 2 dummy atoms to mantain the planar square geometry of the metal. 

I have built my system with no dummy atoms, using GAFF and converted it into Gromacs, so now I have a .gro and a .top file.

I have introduced then the dummy atoms, in the .gro and in the topology file, but 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? 


Thank you very much for your help.


Best wishes,


Dr. Rebeca Garcia

Universidad de A Coruña

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