protein instability

From: sripad chandan (
Date: Mon Nov 10 2008 - 21:27:18 CST

I am doing a simulation of protein of 86 residues with PBC (water layer of

First i am doing the minimization in 4 steps (2fs)

1. Fix all heavy atoms and minimize hydrogen only (O of water fixed). 5000

2. Now release side chains (fix the backbone only) and minimize to same
degree.5000 ts

3. Now release all atoms except Calpha and minimize to same degree.5000 ts

4. Release all constraints and minimize . 5000 ts

 In equilibrium (NPT) steps (2fs)

1) Equilibrate the fixed protein in the NPT ensemble for 50 ps heating
the protein gradually from 0 to 310K. (lengevin parameter on)

2) Equilibration for 200 ps at 310 K with harmonic constraints
gradually reduced to zero. (changing the "constraint scaling")

3) Continuous equilibration for 5 ns. ?

But after a simulation of about 3 ns one end of protein (2 residues only but
most ofthe protein remain inside) comes out of the waterbox.

the RMSD is as high as 5.5

is there any problem with the water layer or temperature?



Sripad Chandan Patnaik
Research Assistant
National Institute of Technology, Rourkela

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