Similar atomname for two different atomtypes?

User discussions
1

Dear gromacs users,

I am currently working on running a simulation for a small molecule: alcohol and water binary mixture. I have parametrized the alcohol molecule using acpype for obtaining amber ff compatible parameters and the final simulation of the alcohol+water system was run using generalized amber ff. However, I recently checked that two of the aiphatic hydrogen atoms of the alcohol and the hydroxyl hydrogen atoms of the water molecules, have the same atom name in their corresponding gro and itp files. The atomname in the alcohols are often very randomly assigned as majority of the organic molecule structures are either downloaded from some resource, e.g., pubchem, atb or explicitly the molecule is modeled using gaussian or avogadro.

My question is that for repetitive entries of atomanmes (for two different atoms), is that going to be fine? If I am not mistaken, gromacs issues a warning when a single atomtype is defined multiple times. But as I see that gromacs does not issue a warning for repetitive entries of atomname maybe given that atomtypes are not repeated.

2

Apart from pdb2gmx and selections, atomnames are not used in GROMACS except for printing. So you can choose whatever names you want. pdb2gmx assigns atomtypes and interactions by atomname and residue type, so for pdb2gmx atomnames need to be unique within a residue.

3

Thank you for your response Prof. Hess. Now I understand that if I am not using pdb2gmx and using an itp with already defined atomtypes etc., then atomnames can be anything as long as different atomtypes are defined and same atomtype should not be defined more than once.