On Thu, 21 Feb 2008 14:54:35 +0530 (IST)
[EMAIL PROTECTED] wrote:
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.
one paper that might be interest:
Wang and Wade, JCTC-2007 3:1476
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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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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