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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