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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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