[gmx-users] center the system on specific atoms type

R.Perez Garcia r.perez.garcia at student.rug.nl
Thu Mar 15 11:16:55 CET 2012

 Dear all,
I am running a simulation in of a fullerene in different solvents. I would like to keep the fullerene somehow centred in the box, so I changed co comm_grps =  System to mm_grps  =  FUL. 
If I do this the following error pop up:

There are:   395      Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...

NOTE 1 [file short1.mdp]:
  4728 atoms are not part of any of the VCM groups

WARNING 1 [file short1.mdp]:
  Some atoms are not part of any center of mass motion removal group.
  This may lead to artifacts.
  In most cases one should use one group for the whole system.

I am not sure if it is possible to tackle this.... 
Any suggestion would be welcomed.
Best regards: R
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