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

[Yu Du]

Hi Robert,

I have only used MDTraj for distance calculation between trajectories, no experience in parameters extraction. If MDTraj cannot satisfy your custom requirement, that I recommend VMD Tcl scripts to extract related information. It probably takes you a week to master the VMD system, but it deserves the efforts and time.

Cheers,

Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China.
Zip: 200032, Tel: (86) 021 5492 5275
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Robert Cordina <robert.cordina at strath.ac.uk>
Sent: Friday, April 17, 2020 01:37
To: gmx-users at gromacs.org <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Measuring bond distances, angles and dihedrals

Hi,

I've carried out a number of equilibrations and I now want to extract bond distances, bond angles and dihedrals from the resulting trajectories.  I'm using MDTraj to do this, which is working perfectly fine, however I'm not too happy with the results as they are not exactly how I want them.  I am using modelling quite small molecules, so I'm only measuring distances, angles and dihedrals a few atoms apart.  I'm doing this to start parameterising a new coarse-grained force field, and for example I get a bond angle of 160 degrees, when really it should be 180 degrees.  This is happening because I'm calculating the angle between specific atoms spaced only 3-4 atoms apart which might be on opposite sides of a straight chain of carbon atoms.  What I'd like to get out is the angle between the centroid of the groups of atoms that would form the coarse-grained beads.

Does anyone have any suggestions if this can be done in GROMACS, or in any Python library which works with GROMACS?

Thanks,

Robert
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