[gmx-users] A question about dihedral angles

Amir Marcovitz amarcovitz at gmail.com
Wed Feb 10 20:52:52 CET 2010

Hi all,

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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