[gmx-users] [EXTERNAL] Re: Measuring bond distances, angles and dihedrals

[Smith, Micholas D.]

I had forgotten about gmx pairdist, thank you for the reminder Justin. 

Also a word of warning for the original suggestion of using VMD. Two words of caution: 1) Be sure you unwrap your trajectories carefully before using vmd for the analysis (otherwise you may get odd 'spikes' in your distances due to the PBC), 2) Since vmd doesn't have any topology information, all of the bonds/angles/dihedral information is inferred, so make sure you are using your selections very carefully. 

-Micholas

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Justin Lemkul
Sent: Friday, April 17, 2020 9:23 AM
To: gmx-users at gromacs.org
Subject: [EXTERNAL] Re: [gmx-users] Measuring bond distances, angles and dihedrals



On 4/17/20 9:19 AM, Smith, Micholas D. wrote:
> Gmx chi I believe gives the dihedral information. Distances can be 
> obtained from gmx mindist

More generally, gmx angle or gangle are for angles and dihedrals (and gangle can calculate angles between planes and/or vectors as may be required here), gmx distance or gmx pairdist for bond lengths.

-Justin

> -Micholas
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se 
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Yu Du
> Sent: Friday, April 17, 2020 5:32 AM
> To: gmx-users at gromacs.org
> Subject: [EXTERNAL] Re: [gmx-users] Measuring bond distances, angles 
> and dihedrals
>
> Hi Robert,
>
> Yes, I always use VMD Tcl scripts to analyse trajectories after MD simulation. The bond distances and angles between atom cluster centroids can definitely be extracted by VMD.  But I don't know how to extract them using GROMACS. If your project is not so urgent, VMD is your choice. It is fairly flexible and can almost satisfy all your requirements.
>
> Cheers,
> Yu

--
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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