[gmx-users] No group in index file?

Justin Lemkul jalemkul at vt.edu
Thu Oct 31 21:26:24 CET 2013

On 10/31/13 4:22 PM, Xu Dong Huang wrote:
> @ Justin,
> That doesn’t sound very good. I tried it as he suggested using make_ndx, it
> seems to work, but it’s not reporting the result I want. When I use g_angle
> using the index i created, I chose the group I want to assess (My compound is
> very simple in Martini, it’s only represented by 3 atoms) and it reports back
> to me 1 angle value. However, I wish to assess the angle between atom 1 & 2,
> 2&3 and 1&3. How should I go about achieving that?

If you have 3 atoms/particles, there can be only one angle, by definition.

Do you have an [angles] directive in the topology?  That's how mk_angndx parses 
the .tpr file - by creating groups of similar angles based on theta and ktheta. 
  If your model doesn't specify any angle potential, then mk_angndx will bail 
out and return nothing, though it should probably do that in a more elegant way 
than producing an empty file.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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