GROMACS version: 2021.1
GROMACS modification: No
Dear GROMACS users/developers,
I am trying to do some simulated tempering simulations on a protein with explicit solvent (TIP4P-D).
I am using a temperature range of ~ 293 to 410 K. However, the temperature doesn’t change during the simulation and the system stays at the lowest temperature of 293 K. The same can be seem in the final weights.
MC-lambda information
Wang-Landau incrementor is: 1
N Temp.(K) Count G(in kT) dG(in kT)
1 293.150 2000 0.00000 2000.00000 <<
2 299.000 0 2000.00000 0.00000
3 304.850 0 2000.00000 0.00000
4 310.700 0 2000.00000 0.00000
5 316.550 0 2000.00000 0.00000
6 322.400 0 2000.00000 0.00000
7 328.250 0 2000.00000 0.00000
8 334.100 0 2000.00000 0.00000
9 339.950 0 2000.00000 0.00000
10 345.800 0 2000.00000 0.00000
11 351.650 0 2000.00000 0.00000
12 357.500 0 2000.00000 0.00000
13 363.350 0 2000.00000 0.00000
14 369.200 0 2000.00000 0.00000
15 375.050 0 2000.00000 0.00000
16 380.900 0 2000.00000 0.00000
17 386.750 0 2000.00000 0.00000
18 392.600 0 2000.00000 0.00000
19 398.450 0 2000.00000 0.00000
20 404.300 0 2000.00000 0.00000
21 410.150 0 2000.00000 0.00000
The total simulation length was 4 ns just to check if everything was working as expected.
My mdp file is pasted below. I would really appreciate any suggestions to make the system explore other temperatures.
Amin.
mdp file
integrator = md-vv
dt = 0.002
nsteps = 2000000
nstxtcout = 2500
nstvout = 250000
nstfout = 250000
nstcalcenergy = 1000
nstenergy = 1000
nstlog = 1000
;
cutoff-scheme = Verlet
nstlist = 20
rlist = 1.0
coulombtype = pme
rcoulomb = 1.0
vdwtype = Cut-off
;vdw-modifier = Force-switch
;rvdw_switch = 1.0
rvdw = 1.0
DispCorr = EnerPres
;
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 293.15 293.15 ; reference temperature, one for each group, in K
;
pcoupl = berendsen
pcoupltype = isotropic
tau_p = 5.0
compressibility = 4.5e-5
ref_p = 1.0
;
constraints = h-bonds
constraint_algorithm = LINCS
lincs-iter = 2
lincs-order = 6
continuation = yes
;
nstcomm = 100
comm_mode = linear
comm_grps = SYSTEM
;
refcoord_scaling = com
;Simulated tempering
nstexpanded = 1000
simulated-tempering = yes
sim-temp-low = 293.15
sim-temp-high = 410.15
simulated-tempering-scaling = linear
init_lambda_state = 0
temperature_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
lmc-stats = wang-landau
lmc-move = metropolized-gibbs
lmc-weights-equil = wl-delta
weight-equil-wl-delta = 0.001
wl-scale = 0.7
wl-ratio = 0.8
init-wl-delta = 1.0
wl-oneovert = yes