[gmx-users] A question about dihedral angles
amarcovitz at gmail.com
Wed Feb 10 20:52:52 CET 2010
i think my question is kind of trivial but i'll ask it any way:
suppose you have atoms that are arranged on the XY plane in a square
lattice arrangment with a spacing of 1. you bond them , add angles etc. and
now you want to add proper dihedral angles using function 1.
What i know, is that the dihedral angle 'phi' between a quartet of atoms
i,j,k,l is the angle between the two surface i,j,k and j,k,l. (i think this
is also written in the manual..)
yet, i experience some problems with a system similar to the one i
described above - i.e., the planar geometry of the atoms gets twisted until
it blows up which make me confused and think that i may did some mistakes in
defining these angles in the [ dihedrals ] section of the topology file.
it could realy be useful if someone can tell me the value of the dihedral
phi for the following quartets (given the x,y coordinates):
1) i (0,0) , j (0,1) , k (1,1) , l(1,2)
2) i(0,0) , j (1,0) , k(2,0) , l(3,0)
3) i(0,0) , j(1,0) , k (2,0), l(2,1)
4 ) i(0,0) , j(1,0) , k(1,1) , l(0,1)
i think that 1 is 180 degrees , and 2,3,4 are 0 degrees am i right? is
there a difference between 0 and 180?
(i used a multipilicty of 2)
i.e., it looks like
[ dihedrals ]
; ai aj ak al funct phi cp mult
7 1 2 3 1 0.000000e+00 3.347200e+01 2.000000e+00
14 8 9 15 1 1.800000e+02 3.347200e+01 2.000000e+00
and so on..
sorry for the bizzare question..
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