[gmx-users] unfolding a protein

[Siavoush Dastmalchi]

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