[gmx-users] Rule for atom names in GROMACS

Ebert Maximilian m.ebert at umontreal.ca
Fri May 29 14:24:25 CEST 2015

Hi there,

While building my own topology I was wondering if the atom name is only used to link .gro atoms with .top entries. The behaviour of an atom is defined by the atom type and the atom name should not have any effect on the simulation right? So if I choose an atom name for a carbon as C, C11 or C2 the outcome should be the same as long as the atom has the same name in .gro and .top and the same type. Am I correct here? So atom names are used to link .top and .gro and later in visualization softwares like VMD to place a carbon atom in the GUI instead of something else. Correct?

Finally I was wondering if the atom name needs to be unique within a molecule.

Thanks for the clarification,


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