[gmx-users] elastic network model -protein contracting

[mohan maruthi sena]

Hi all,
           I want to prepare a  basic elastic network model  (tirion
model) of protein. For this i have taken only C-alpha atoms of the
protein

    and considered only  streching potential(k.(b-b0)^2)) and removed
rest of angle,dihedral,non bonded interactions. I have mentioned a
bond between C-alpha and C-alpha in ffbonded.itp file with equilibrium
distance 0.39 nm and force constant of 96400 kj/nm2 .  I don't
performed any minimisation ,just done equilibration  and production.
When i load final trajectory file(after production run) the protein
contracts after first frame ,some of the atoms are over one another
overlapping one over the other. Please help me to solve this problem.



Thanks in advance,
Mohan.