[gmx-users] Rule for atom names in GROMACS

Justin Lemkul jalemkul at vt.edu
Fri May 29 14:44:59 CEST 2015

On 5/29/15 8:22 AM, Ebert Maximilian wrote:
> 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.

Only pdb2gmx and grompp care about atom names.  pdb2gmx needs unique names to 
unambiguously define bonded structure.  grompp checks names to make sure the 
user hasn't butchered the agreement between coordinates and topology.  mdrun 
couldn't care less if your atoms are named Fred and Bob; it only cares about 
topological interactions.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list