Re: protein instability

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Nov 11 2008 - 10:26:36 CST

Hi Chandan,
two things:
-please look at the list for previous questions involving the protein
protruding from the box. It is very frequently asked.
-With that said, 5A is an extremely thin layer of water, and you risk
interactions between adjacent periodic images of your protein.
Peter

sripad chandan wrote:
> Friends,
> I am doing a simulation of protein of 86 residues with PBC (water
> layer of 5A).
>
> First i am doing the minimization in 4 steps (2fs)
>
> 1. Fix all heavy atoms and minimize hydrogen only (O of water fixed).
> 5000 ts
>
> 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?
>
> thanks.
>
> chandan
>
>
>
>
>
> --
> Sripad Chandan Patnaik
> Research Assistant
> National Institute of Technology, Rourkela
> +91-9861668977

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