[gmx-users] Need Help on Simulated annealing (Implicit Solvation)

[Raghuvir R. S. Pissurlenkar]

Hi
I have tried to write a grompp.mdp file for simulated annealing of a peptide (~30 aa) in implicit solvent.

Please someone could tell me if the parameters set are fine for the same.

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; Preprocessing
define = -DFLEXIBLE

; Run control
integrator = md
dt = 0.002
nsteps = 500000; 1 ns
comm-mode = angular
nstcomm = 1000
comm-grps = system

; Langevin dynamics
bd-fric = 0
ld-seed = 1993

; Output control
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000

; Neighbor searching
cutoff-scheme = group
nstlist = 10
ns-type = simple
pbc = no
rlist = 0

; Electrostatics
coulombtype = cut-off
rcoulomb = 0

; VdW
vdwtype = cut-off
rvdw = 0

; Temperature coupling
tcoupl = v-rescale
tc-grps = Protein
tau-t = 0.5
ref-t = 300.0

; Pressure coupling
pcoupl = no

; Simulated annealing
annealing = single
annealing-npoints = 1
annealing-npoints = 0 10 20 30 40 50
annealing-temp = 300 320 340 360 380 400

; Velocity generation
gen-vel = yes
gen-temp = 300.0
gen-seed = 173529

; Bonds
constraints = all-bonds
constraint-algorithm = P-LINCS
lincs-order = 4
lincs-iter = 1

; Implicit solvent
implicit-solvent = GBSA
gb-algorithm = OBC
nstgbradii = 1.0
rgbradii = 1.0
gb-epsilon-solvent = 80
gb-saltconc = 0
gb-obc-alpha = 1
gb-obc-beta = 0.8
gb-obc-gamma = 4.85
gb-dielectric-offset = 0.009
sa-algorithm = Ace-approximation
sa-surface-tension = –1

-----------------------------------------------------------------------------------------------

Thanks and Regards


Raghuvir