From: Nash, Anthony (
Date: Mon Feb 29 2016 - 00:56:29 CST

Hi all,

I defined a set of complete new atom types in Gromacs (atom type, atom name, along with all the necessary forcefield parameterisation) but now I wish for the trajectory to be visualised in VMD. Currently, the gromacs-own glycine terminal residues appears as normal, however, my new fragment is all one colour, with a strange set of bonds (obviously not included in the MD simulation, simply a VMD artefact of using a distance based bond assignment over atom types it does not recognise). Any suggestions would be great.

Many thanks

Dr Anthony Nash
Department of Chemistry
University College London