[gmx-users] Simulated Annealing Protocol...

[rama david]

Dear Gromacs Specialists,
                I am very novice to Molecular Simulation study.
 I am using GROMACS 4.5.4 version .
I completed some GROMACS tutorials , I not found any
tutorial on Simulated Annealing..
If Any one know the link please give me it..

I make my  protocol to work on simulated annealing as follow ...
(I am not writing in detail sorry for that )
1.  pdb2gmx ...
2. editconf
3. Solvent Addition
4.  Ion addition
5. Energy minimisation
6. simulated annealing
 mdp for simulated annealing is as follow...

; 7.3.3 Run Control
title                   = simulated run

integrator              = md                    ; md integrator
tinit                      = 0                     ; [ps] starting time for run
dt                         = 0.002                 ; [ps] time step
for integration
nsteps                  = 5000000               ; maximum number of
steps to integrate, 0.002 * 5000000 10 ns
comm_mode         = Linear                ; remove center of mass translation
comm_grps           = Protein Non-Protein   ; group(s) for center of
mass motion removal

; 7.3.8 Output Control
nstxout                 = 100       ; [steps] freq to write
coordinates to trajectory
nstvout                 = 100       ; [steps] freq to write velocities
to trajectory
nstfout                 = 100       ; [steps] freq to write forces to trajectory
nstlog                  = 100           ; [steps] freq to write
energies to log file
nstenergy               = 100           ; [steps] freq to write
energies to energy file
nstxtcout               = 500           ; [steps] freq to write
coordinates to xtc trajectory
xtc_precision           = 500          ; [real] precision to write xtc
trajectory
xtc_grps                = System        ; group(s) to write to xtc trajectory
energygrps              = System        ; group(s) to write to energy file

; 7.3.9 Neighbor Searching
nstlist                 = 5             ; [steps] freq to update neighbor list
ns_type                 = grid          ; method of updating neighbor list
pbc                     = xyz           ; periodic boundary conditions
in all directions
rlist                   = 1.0           ; [nm] cut-off distance for
the short-range neighbor list

; 7.3.10 Electrostatics
coulombtype             = PME           ; Particle-Mesh Ewald electrostatics
rcoulomb                = 1.0           ; [nm] distance for Coulomb cut-off

; 7.3.11 VdW
vdwtype                 = cut-off       ; twin-range cut-off with
rlist where rvdw >= rlist
rvdw                    = 1.4           ; [nm] distance for LJ cut-off
DispCorr                = EnerPres      ; apply long range dispersion
corrections for energy

; 7.3.13 Ewald
fourierspacing          = 0.16          ; [nm] grid spacing for FFT
grid when using PME
pme_order               = 4             ; interpolation order for PME, 4 = cubic
ewald_rtol              = 1e-5          ; relative strength of
Ewald-shifted potential at rcoulomb

; 7.3.14 Temperature Coupling
tcoupl                  = berendson                   ; temperature
coupling with Nose-Hoover ensemble
tc_grps                 = Protein    Non-Protein        ; groups to
couple seperately to temperature bath
tau_t                   = 0.1        0.1                ; [ps] time
constant for coupling
ref_t                   = 5           5               ; [K] reference
temperature for coupling
annealing               = single single
annealing_npoint        = 2  2
annealing_time          = 0 20 0 20
annealing_temp          = 5 333 5 333
; 7.3.15 Pressure Coupling
pcoupl                  =  parrinello-Rahman    ; pressure coupling
where box vectors are variable
pcoupltype              = isotropic             ; pressure coupling in
x-y-z directions
tau_p                   = 2.0                   ; [ps] time constant
for coupling
compressibility         = 4.5e-5                ; [bar^-1] compressibility
ref_p                   = 1.0                   ; [bar] reference
pressure for coupling

; 7.3.17 Velocity Generation
gen_vel                 = yes           ; velocity generation turned off
gen_temp                = 5
; 7.3.18 Bonds
constraints                  = all-bonds     ; convert all bonds to constraints
constraint_algorithm    = LINCS         ; LINear Constraint Solver
continuation               = yes           ; apply constraints to the
start configuration
lincs_order                 = 4             ; highest order in the
expansion of the contraint coupling matrix
lincs_iter                    = 1             ; number of iterations
to correct for rotational lengthening
lincs_warnangle         = 30            ; [degrees] maximum angle that
a bond can rotate before LINCS will complain

My Queries

1. Is My mdp file ok ???..please give me a nice protocol..
2.. Should I have to do position restrained MD before SA(simulated annealing)
    (If yes then what the temp. should I have to used for NVT and NPT
(as in mdp file has lower 5 K and high 300 k  ) )