GROMACS version: 2024.1
GROMACS modification: No
In every simulation I’ve attempted constructing my protein seems to dissociate rapidly, ~35% native contacts in first 50 or so frames at temperatures ranging from 150 to 400 K, I’ve also tried both Amber and CHARMM force fields and from what I’ve been able to find out that seems to stem from equilibration issues. I go through the basic minimization, NVT and NPT equilibration and when I run the final tpr it all goes bad. I’m an undergrad just getting started with GROMACS and I’m not sure what It is that I’m getting wrong or what I could be overlooking. I’m using the mdp from github for the minimization and equilibration steps.
So your point is, it remains stable in NVT and NPT and then dissociates in (NPT) production? What do you change between NPT equlibration and NPT production in terms of .mdp settings?
I believe that’s what’s happening and the only changes I’ve made to my .mdp for the production run is defining some temperature coupling groups, and modify the temperature of the system. Here is the production .mdp settings I’ve been using:
; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/roe
include =
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
define = -DPOSRES
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 2000000
; For exact run continuation or redoing part of a run
init-step = 0
; Part index is updated automatically on checkpointing (keeps files separate)
simulation-part = 1
; Multiple time-stepping
mts = no
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 500
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = -1
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 10
emstep = 0.01
; Max number of iterations in relax-shells
niter = 20
; Step size (ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 500
nstvout = 500
nstfout = 500
; Output frequency for energies to log file and energy file
nstlog = 500
nstcalcenergy = 500
nstenergy = 500
; Output frequency and precision for .xtc file
nstxout-compressed = 500
compressed-x-precision = 1000
; This selects the subset of atoms for the compressed
; trajectory file. You can select multiple groups. By
; default, all atoms will be written.
compressed-x-grps = protein ;testing for better output
; Selection of energy groups
energygrps = protein ;testing for better output, wpot
; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (Verlet: particle based cut-offs)
cutoff-scheme = Verlet
; nblist update frequency
nstlist = 10
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic-molecules = yes
; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-tolerance = 0.005
; nblist cut-off
rlist = 1
; long-range cut-off for switched potentials
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch = 0
rcoulomb = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r = 1
epsilon-rf = 0
; Method for doing Van der Waals
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
; cut-off lengths
rvdw-switch = 0
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Separate tables between energy group pairs
energygrp-table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.16
; FFT grid size, when a value is 0 fourierspacing will be used
fourier-nx = 0
fourier-ny = 0
fourier-nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
implicit-solvent = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = yes
nsttcouple = -1
nh-chain-length = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc-grps = Protein Non-Protein ; sd integrator still requires explicit groups
; Time constant (ps) and reference temperature (K)
tau_t = 2 2
ref_t = 175 175
; pressure coupling
pcoupl = berendsen
pcoupltype = isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = com
; OPTIONS FOR QMMM calculations
QMMM = no
; Groups treated with MiMiC
QMMM-grps =
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing =
; Number of time points to use for specifying annealing in each group
annealing-npoints =
; List of times at the annealing points for each group
annealing-time =
; Temp. at each annealing point, for each group.
annealing-temp =
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen-temp = 300
gen-seed = -1
; OPTIONS FOR BONDS
constraints = h-bonds
; Type of constraint algorithm
constraint_algorithm = lincs
; Do not constrain the start configuration, ‘yes’ when using past run data (npt, nvt, etc.)
continuation = yes
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix
lincs_order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs_iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp-excl =
; WALLS
; Number of walls, type, atom types, densities and box-z scale factor for Ewald
nwall = 0
wall-type = 9-3
wall-r-linpot = -1
wall-atomtype =
wall-density =
wall-ewald-zfac = 3
; COM PULLING
pull = no
; AWH biasing
awh = no
; ENFORCED ROTATION
; Enforced rotation: No or Yes
rotation = no
; Group to display and/or manipulate in interactive MD session
IMD-group =
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) and S to energy file
nstorireout = 100
; Free energy variables
free-energy = no
couple-moltype =
couple-lambda0 = vdw-q
couple-lambda1 = vdw-q
couple-intramol = no
init-lambda = -1
init-lambda-state = 0
delta-lambda = 50
nstdhdl = 50
fep-lambdas = 0
mass-lambdas = 0
coul-lambdas = 0
vdw-lambdas = 0
bonded-lambdas = 0
restraint-lambdas = 0
temperature-lambdas = 0
calc-lambda-neighbors = 1
init-lambda-weights =
dhdl-print-energy = no
sc-alpha = 0
sc-power = 1
sc-r-power = 6
sc-sigma = 0.3
sc-coul = no
separate-dhdl-file = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing = 0.1
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
deform =
; simulated tempering variables
simulated-tempering = no
simulated-tempering-scaling = geometric
sim-temp-low = 300
sim-temp-high = 300
; Ion/water position swapping for computational electrophysiology setups
; Swap positions along direction: no, X, Y, Z
swapcoords = no
adress = no
; User defined thingies
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
; Electric fields
; Format for electric-field-x, etc. is: four real variables:
; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps),
; and sigma (ps) width of the pulse. Omega = 0 means static field,
; sigma = 0 means no pulse, leaving the field to be a cosine function.
electric-field-x = 0 0 0 0
electric-field-y = 0 0 0 0
electric-field-z = 0 0 0 0
; Density guided simulation
density-guided-simulation-active = false
You have position restraints turned on in your production run, I hope that’s desired? And running NPT at 175K, that’s close to liquid ethane - are you sure these are production settings?
It would be much more convenient if you just provided a diff between the two .mdp files though.