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

[Robert Cordina]

Thanks all, I'll investigate these options.

Best regards,

Robert

-----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: 17 April 2020 14:23
To: gmx-users at gromacs.org
Subject: 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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