[gmx-users] Is simulated annealing mdp ok

[Mijiddorj Batsaikhan]

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"

2. Is mdp file correct?

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