Hi,
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
Spain
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