Sorry for the long mail but-
From the manual:
“For example, imagine the 1-3 weighting factor is set to 0.5 and you have a linear molecule with 4 atoms and bonds as follows: 1-2-3-4. If your data file defines 1-2-3 as an angle, but does not define 2-3-4 as an angle or 1-2-3-4 as a dihedral, then the pairwise interaction between atoms 1 and 3 will always be weighted by 0.5”
I could not understand it. the weightage in special_bond keyword is applied to defined angles (1-3 interactions) or all 1-3 interactions which are not defined in my input file? It kind of sound counter intutive to me that special_bond will alter angle_coeff values. Am i right?
Background:
I am trying to run dynamics on a box filled with a solvent (NMP). But molecules are not moving. They are vibrating, and if i leave some empty space they will rush to fill it but that’s it after that whole system becomes stationary with just vibrations but no movement.
My understanding of special_bonds is that it gives weightage to intra-molecular interactions, hence things like density shall remain unaffected if i play around with it. but with:
special_bonds lj 0 0 1 coul 0 1 1
i am getting density of 0.7 gm/cc and bond lengths comparable to ab-initio calculations
special_bonds lj 0 0 0 coul 0 1 1
i am getting density 0.95 gm/cc but molecule is little puckered up
if interested in input script: http://pastebin.com/wapPfspy
force filed used was universal force field