[gmx-users] Peptide folding simulation

[bharat gupta]

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.

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 .




----------------
BHARAT