From: Josh Vermaas (
Date: Mon Feb 29 2016 - 09:50:45 CST

Bonding isn't in a gro file. Those only have coordinates, so vmd will still guess bonding based on distance unless you provide the bonding info yourself, which is why I was trying to steer you to formats that provide topology.

On Feb 29, 2016 6:51 AM, "Nash, Anthony" <> wrote:
Hi Josh,

I’ve essentially written my own forcefield from QM data etc., I think unless there is a soft coded list that VMD reads (as surely it must know that C and CA are both carbons and how to render them), I’ll probably need to convert the .trr to a .gro and search and replace my new atom names e.g.,  DC1, DC2, etc.. DN1, DN2, etc.. To something more common e.g., C and N. 


Dr Anthony Nash
Department of Chemistry
University College London

From: Josh Vermaas <>
Date: Monday, 29 February 2016 14:43
To: "Nash, Anthony" <>
Cc: "" <>
Subject: Re: vmd-l: New atom types in VMD

Hi Anthony,

Fundamentally, Gromacs stores the topology in either the tpr file or the top file. The tpr format changes with every gromacs version, so a reader isn't available. There are scripts I think that can load in the data from a top file (I'm traveling and can't find them, but the Martini folks do this stuff all the time.). Alternatively, you can convert the trajectory to a tng file with Gromacs tools. These files contain topology information, and can be read with vmd when compiled appropriately.

Good luck!
Josh Vermaas

On Feb 28, 2016 10:56 PM, "Nash, Anthony" <> wrote:
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