[gmx-users] elastic network model -protein contracting
Mark.Abraham at anu.edu.au
Wed Aug 22 05:13:57 CEST 2012
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
> 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.
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