[gmx-users] Peptide folding simulation

[intra\sa175950]

Hi 

To see folding events in your (very) long peptide in explicit solvent,
without doing long MD (> 100 ns), you will need to use more complex MD
approach such as REMD or metadynamics. REMD is implemented in gromacs, but
for the latter one, you can use plumed with GROMACS.

See for example http://www.plumed-code.org/

HTH 

Stephane

 

------------------------------

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