[gmx-users] g_angle between three atoms

Justin Lemkul jalemkul at vt.edu
Fri Nov 28 19:29:06 CET 2014

On 11/28/14 11:20 AM, Victor Rosas Garcia wrote:
> My guess is that g_angle is taking the atom order for the bond angle
> from the topology.

g_angle does not read anything from a topology; in fact, none is even passed to 
the program.  The OP needs to quantitatively define the observations.  The index 
groups should all (presumably) produce different results, but the claim that the 
correct angle isn't even being measured doesn't even make much sense.  Programs 
only do what you tell them.


> Hope this helps
> Victor
> 2014-11-28 8:21 GMT-06:00 Cyrus Djahedi <cyrusdja at kth.se>:
>> Hi all. I'm interested in calculating a specific angle between three atoms situated in adjacent cellulose polymer chains. So I made the following index groups:
>> Group     8 (a_3194_a_2348_a_4463) has     3 elements
>> Group     9 (a_4463_a_3194_a_2348) has     3 elements
>> Group    10 (a_2348_a_4463_a_3194) has     3 elements
>> Notice how its the same atoms arranged in different order, yet GROMACS calculates the same angle over and over, the one Im NOT interested in. Any tips?
>> / Cyrus
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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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