[gmx-users] Simulated Annealing Protocol...
bipin singh
bipinelmat at gmail.com
Sat Mar 17 19:14:32 CET 2012
Hello users,
I have also got a doubt regarding SA. My doubt is, whether it is
correct to do SA in NVT? I mean increasing the temperature to desired
temperature during SA (with position restraints) with no pressure
coupling. Afterwards NPT(with position restraints) then final
production run in NPT
On Sat, Mar 17, 2012 at 19:56, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> --
> ========================================
>
> 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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--
-----------------------
Regards,
Bipin Singh
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