[gmx-users] Is simulated annealing mdp ok

[Justin Lemkul]

On 3/1/16 5:30 AM, Mijiddorj Batsaikhan wrote:
> Dear gmx users,
>
> I would like to explore two proteins interactions in water using simulated
> annealing. in my topology file, my proteins are named Protein and Protein2.
> I have following 2 hesitations:
>
> 1. How to set energy groups in mdp file?
>
> I wrote
>       "define = Protein Non-Protein"
>

This does nothing.  What are you trying to achieve?

> 2. Is mdp file correct?
>

Correct by what definition?  What are you trying to do?  What force field are 
you using?  It appears syntactically sound, but that's different from "correct."

-Justin

> title = Simulated Annealing
> define = -DPOSRES ; restrain protein
> energygrps = Protein Non-Protein
> ; Run parameters
> integrator = md ; leap-frog integrator
> dt = 0.002 ; 2 fs
> nsteps = 25000000 ; 50000 ps
> ; Bond parameters
> continuation = no ; starting up
> constraints = all-bonds ; constrain all bond lengths
> constraint-algorithm = lincs ; holonomic constraints
> lincs-iter = 1 ; accuracy of LINCS
> lincs-order = 4 ; also related to accuracy
> ; Output control
> nstxout = 1000 ; save coordinates every 2 ps
> nstvout = 1000 ; save velocities every 2 ps
> nstfout = 1000 ; save forces every 2 ps
> nstenergy = 1000 ; save energies every 2 ps
> ; Neighborsearching
> nstlist = 5 ; 10 fs
> ns_type = grid ; search neighboring grid cells
> rlist = 1.2 ; short-range neighborlist cutoff (nm)
> rcoulomb = 1.2 ; short-range electrostatic cutoff (nm)
> rvdw = 1.2 ; short-range van der Waals cutoff (nm)
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing  = 0.16 ; grid spacing for FFT
> ; Temperature coupling is on in three groups
> Tcoupl = Berendsen ; Weak coupling
> tc_grps = Protein Non-Protein ; two coupling groups
> tau_t = 0.1 0.1 ; time constant, in ps
> ref_t = 310 310 ; reference temperature, one for each group, in K
> ; Pressure coupling
> Pcoupl = Berendsen    ; Weak coupling
> Pcoupltype = semiisotropic    ; uniform scaling of x-y vectors, independent
> z
> ref_p = 1.0 1.0    ; reference pressure, x-y, z (in bar)
> compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1
> ; Generate velocities is off
> gen_vel = no ; Velocity generation is off
> ; Periodic boundary conditions are on in all directions
> pbc    = xyz ; 3-D PBC
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme
> ; Simulated annealing
> annealing = periodic periodic    ; periodic sequence of points for each
> T-coupling group
> annealing_npoints = 10 10        ; two points - start and end temperatures
> annealing_time = 0 5000 10000 15000 20000 25000 30000 35000 40000 50000 0
> 5000 10000 15000 20000 25000 30000 35000 40000 50000    ; time frame of
> heating
> annealing_temp = 0 100 100 200 200 300 300 400 400 310 0 100 100 200 200
> 300 300 400 400 310  ; start to end temperatures
> ; COM motion removal
> ; These options remove motion of the protein/bilayer relative to the
> solvent/ions
> nstcomm = 1
> comm-mode = Linear
> comm-grps = Protein Non-Protein
>
>
>
>
>
>
> Best regards,
>
> Mijiddorj
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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