[gmx-users] A question about dihedral angles
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Feb 11 03:52:46 CET 2010
On 11/02/10 06:52, Amir Marcovitz wrote:
> 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.
I think this is all covered in chapter 4 of the manual.
Mark
> 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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