On 7/9/12 12:02 AM, bharat gupta wrote:
Hi,
I have been trying to study folding of a peptide 24 residues long. I
did a simulation of 50 ns with explicit solvent, CHARMM FF, but I
was not able to find even a single folding event. Then I decided use
explicit solvent for simulation and I again simulated the peptide for
100 ns . This time again I ended with no folding events.
I know that in case of explicit solvent , a 50ns simulation time is
not enough to observe anything. But I did it to see the initial
behavior of the peptide in water. In take many random like
conformation but doesnot fold into a desired beta-hairpin. For the
explicit solvent simulation, I followed the lysozyme tutorial
parameters.
You shouldn't. The .mdp settings are appropriate for OPLS-AA, not CHARMM.
For implicit solvent simulation, I used the following parameters for
Energy minimization :
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.001 ; ps
nsteps = 30000
vdwtype = cut-off
coulombtype = cut-off
pbc = no
nstlist = 0
ns_type = simple
rlist = 0 ; this means all-vs-all (no cut-off),
which gets expensive for bigger systems
rcoulomb = 0
rvdw = 0
comm-mode = angular
comm-grps = Protein
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 5.0
emstep = 0.01
;
; Implicit solvent
;
implicit_solvent = GBSA
gb_algorithm = Still ; HCT ; OBC
nstgbradii = 1
rgbradii = 0 ; [nm] Cut-off for the calculation of the
Born radii. Currently must be equal to rlist
gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent
; gb_saltconc = 0 ; Salt concentration for implicit
solvent models, currently not used
sa_algorithm = Ace-approximation
sa_surface_tension = -1
For MD I used the following : -
define = -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES
constraints = none
integrator = md
dt = 0.001 ; ps
nsteps = 1000000000 ; 100000 ps = 100 ns
nstcomm = 10
nstcalcenergy = 10
nstxout = 1000 ; frequency to write coordinates to output
trajectory
nstvout = 0 ; frequency to write velocities to output
trajectory; the last velocities are always written
nstfout = 0 ; frequency to write forces to output
trajectory
nstlog = 1000 ; frequency to write energies to log
file
nstenergy = 1000 ; frequency to write energies to edr file
vdwtype = cut-off
coulombtype = cut-off
pbc = no
nstlist = 0
ns_type = simple
rlist = 0 ; this means all-vs-all (no cut-off), which
gets expensive for bigger systems
rcoulomb = 0
rvdw = 0
comm-mode = angular
comm-grps = system
optimize_fft = yes
; V-rescale temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1
tc_grps = system
ref_t = 300
; Pressure coupling is off
Pcoupl = no
; Generate velocites is on
gen_vel = yes
gen_temp = 300
gen_seed = -1
;
; Implicit solvent
;
implicit_solvent = GBSA
gb_algorithm = Still ; HCT ; OBC
nstgbradii = 1
rgbradii = 0 ; [nm] Cut-off for the calculation of the
Born radii. Currently must be equal to rlist
gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent
; gb_saltconc = 0 ; Salt concentration for implicit
solvent models, currently not used
sa_algorithm = Ace-approximation
sa_surface_tension = -1
So, finally I want to know where have I gone in my simulation
experiments, both implicit and explicit ?? ... Please reply .
What evidence do you have that you should expect to see a folding event in such
a short time? Most people will use more extensive sampling methods like REMD to
observe peptide folding.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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