GROMACS version: 2022.1
GROMACS modification: No
Dear users,
I need to use a simulated annealing protocol in order to understand the “important” interactions ligand/protein. Checking in the literature I found out that many researcher use a vdW scale factor during the cooling phase of the simulated annealing, in details they write: “Successively temperature was linearly reduced to 300 K in 5 ps, and, concurrently, the vdW scale factor have been similarly increased from its initial value (0.1) to its final value (1.0)”
From what i understood the point is to let the ligand “free” during the firsts moments of the cooling phase and than slowly slowly increase the restraints.
I’d like to know how to setup the .mdp file.
For now I arrived here, but I’m not sure that these parameters will give me the desidered result.
Here my .mdp file (I’m not sure about the vdW section).
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 2500000 ; 2 * 2000000 = 5000 ps (5 ns)
dt = 0.002 ; 2 fs
; Output control
nstxout = 0 ; suppress bulky .trr file by specifying
nstvout = 0 ; 0 for output frequency of nstxout,
nstfout = 0 ; nstvout, and nstfout
nstenergy = 1000 ; save energies every 2.0 ps
nstlog = 1000 ; update log file every 2.0 ps
nstxout-compressed = 1000 ; save compressed coordinates every 2.0 ps
compressed-x-grps = System ; save the whole system
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Van der Walls
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 0.1
rvdw = 1
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_NON1 Water ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
; Simulated annealing
annealing = periodic periodic
annealing_npoints = 6 6
annealing_time = 0 10 18 22 42 50 0 10 18 22 42 50
annealing_temp = 300 300 500 500 300 300 300 300 500 500 300 300