[gmx-users] Simulated Annealing Protocol...

[Justin A. Lemkul]

rama david wrote:
> Hi Gromacs Specialist,
>                Thank you Justin For your reply.
> I run one Simulated Annealing) MD after your reply.
> My aim is to find protein conformation and study protein
>  self assembly study ..
> 
> the protocol I follow is as..
> 1.  Upto energy minimisation I followed the general way
> 2.  I did nvt at 277  K(position resstrain)
> 3.  I did npt at 277   k  ((Position Restrain  )
>  4. then I did the SA  (I removed Position Restrain ) with following mdp
> 
> 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           = 100          ; [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                   ;
> 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                   = 277        277               ; [K] reference
> temperature for coupling
> annealing               = single single
> annealing_npoint        = 2  2
> annealing_time          = 0 50 0 50
> annealing_temp          = 277 333 277 300
> ; 7.3.15 Pressure Coupling
> pcoupl                  = Parrinello-Rahman      ;
> 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                 = no                   ; velocity generation turned off
> gen_temp              = 277
> ; 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
> continuation              =yes
> 
>  so my Queries are
> 1.    As I not  define =  -DPOSRES in SA mdp  is it sound well???,
> should I have to run Production run after my
>        SA run(That means  Is SA is substitute to Production run ??)
> ??? or I have to use   define =  -DPOSRES in my SA mdp ,
>        and then I have to do production run
>  2.   Or as per Justin recommendation  NVT at 277 ,followed by SA
>        (Then I have to use  define = -DPOSRES  in My SA mdp file ,Is it right??)
>       then NPT   afterward Production run ..
> 
>  So what is your suggestion ???

The answers to your question depend entirely upon what you want to do and 
observe.  If you're using SA simply as part of an equilibration protocol (as I 
often do, which was what I based my suggestion upon earlier), then I stick with 
my protocol, which is point #2.

If you're trying to model the behavior of your system in response to a change in 
termperature, then SA is your production run and you would not use position 
restraints.

It is still not clear to me how you wish to use SA or what you hope to observe 
from it, so that's the best I can offer.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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