[gmx-users] How the angle/bond length changes during simulation.

Justin Lemkul jalemkul at vt.edu
Wed Mar 9 16:07:28 CET 2016

On 3/9/16 10:01 AM, Dawid das wrote:
> Dear Gromacs Experts,
> How can I get a plot of a bond length/ valence angle/ dihedral angle during
> simulation
> from *xtc and *.ndx files? I am pretty sure that it is possible, but with
> g_angle
> and g_bond I can get only the distribution.

Get the bond distance(s) with g_dist.

> By the way, when I use
> g_angle -f npt-md2-cent.xtc -n index.ndx -type dihedral -all
> and choose group like this from my index.ndx file:
> [ angles ]
> 969 966 964 960
> 966 964 960 959
> I don't get separate plots for each of two dihedral angles.
> How can I get it?

You are.  That's what -all is for:

"Plot all angles separately in the averages file, in the order of appearance in 
the index file."

Open up angaver.xvg and you will see the average, then the two individual time 



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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