High RMSD in Coarse Grain Simulation of Protein

From: sunita gupta (sunita.bio_at_gmail.com)
Date: Wed Oct 13 2010 - 03:06:22 CDT

Hello everyone,

I am Simulating CG Protein in CG water and ions. The Protocol is as follows:
1. Minimized with constraint of 5 on all atoms except ions.
2. Minimized with constraints of 5 on all beads of protein atoms only.
3. Heated slowly till 300 K with constraints of 5 on protein beads.
4. Equilibrated at NPT condition with damping coefficient of 5 and gradually
removing the constraints from 5 ->4->3->2->1
5. Finally the Production at NPT without any constraints.

I am facing the problem with RMSD, in minimization the rmsd is 0.7 and till
equilibration it goes on increasing smoothly to 1.2 but as it enters the
production phase the rmsd jumps to approx 7 A and angle, dihedral drops
suddenly.

Also, the reverse all-atom pdb does not maintain secondary structure of
protein.

Can any one guide me if I am missing something or following some different
protocol...

Thanks in Advance

-- 
-- 
SUNITA GUPTA

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