[gmx-users] Re: Simulated Annealing Protocol

[Dr. Vitaly V. Chaban]

>  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  ) )
>


Your system will be heated from 5 to 330K during 20ps. If this is what
you want, than it is correct. I would, however, prefer slower heating
in order to make it more realistic.

I see no obvious necessity to start from restrained positions, unless
you are going to performs something specific that you did not describe
above.



Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA