VMD-L Mailing List
From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Feb 29 2016 - 09:50:45 CST
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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.
Josh
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.
Thanks
Dr Anthony NashDepartment of ChemistryUniversity College London
From: Josh Vermaas <vermaas2@illinois.edu>
Date: Monday, 29 February 2016 14:43
To: "Nash, Anthony" <a.nash@ucl.ac.uk>
Cc: "vmd-l@ks.uiuc.edu" <vmd-l@ks.uiuc.edu>
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 VermaasOn 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 thanksAnthony
Dr Anthony NashDepartment of ChemistryUniversity College London
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