[gmx-users] elastic network model -protein contracting

[Mark Abraham]

On 22/08/2012 1:06 PM, mohan maruthi sena wrote:
> 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.

Your model has no way to prevent overlap. You need to fix the model.

Mark