VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Feb 29 2016 - 08:43:14 CST

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" <a.nash@ucl.ac.uk> 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
Anthony 

Dr Anthony Nash
Department of Chemistry
University College London