[gmx-users] unfolding a protein

[mon_sharma at research.iiit.ac.in]

On Wed, 20 Feb 2008, Siavoush Dastmalchi wrote:
Hii!!
The time scale you have chosen is very less to see unfolding in 
proteins of moderate length, because in such a short time u might be able 
to see just local disturbances only, even at temperature of 400K. You need to increase the 
production run time, atleast go for 3n. And you might not need 
constrains of all-bonds to put.

Cheers,
Monika

> Hi there,
>
>
>
> I want to unfold a protein (hen egg white lysozyme) which has got 4 disulfide bounds. I have tried 1 ns of MD at 400 K either in vacuum or hydrated form and it didn't unfold. I know it may need longer time, but it doesn't show any sign of even starting to unfold. I think I am restraining the protein in some way. Please see below the content of ~.mdp file that I use.
>
>
>
> Would you please let me know how I could unfold a protein using an MD simulation?
>
> Do you think unfolding a water soluble protein in vacuum would be faster?
>
>
>
> Cheers, Siavoush
>
>
>
> cpp                      = /lib/cpp
> include                  = -I../top
> integrator               = md
> dt                       = 0.002
> nsteps                   = 500000
> nstxout                  = 1000
> nstvout                  = 1000
> nstlog                   = 100
> nstenergy                = 100
> nstxtcout                = 100
> xtc_grps                 = protein sol
> energygrps               = protein sol
> nstlist                  = 10
> ns_type                  = grid
> rlist                    = 0.8
> coulombtype              = cut-off
> rcoulomb                 = 1.4
> rvdw                     = 1.4
> pbc                      = xyz
> tcoupl                   = berendsen
> tc-grps                  = protein sol
> tau_t                    = 0.1 0.1
> ref_t                    = 400 400
> Pcoupl                   = berendsen
> Pcoupltype               = isotropic
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> gen_vel                  = yes
> gen_temp                 = 400
> gen_seed                 = 173529
> constraints              = all-bonds
>
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