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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