[gmx-users] Unraveling Helix: Simulation Data not in Agreement with Experiment
Matthew Fisher
matthew.fisher at stcatz.ox.ac.uk
Thu Apr 4 15:46:38 CEST 2019
Dear all,
I'm simulating P450 proteins currently and having issues with my simulation data not agreeing with experimentally obtained data. A helix, located immediately above the heme on the distal side, is either unravelling or distorting significantly during production MD runs, whereas crystal structures of identical/similar mutants indicate no such distortion from the WT.
Briefly, I'm using GROMACS 2018.1 and the AMBER99SB-ILDN force field. I'm doing a 2 stage EM: Steepest Descent with a criterion of 500 kJ / mol nm followed by conjugate gradient (100 kJ / mol nm) and then position restrained NVT equilibriation with the v-rescale thermostat (200ps) followed by position restrained NPT with Berendsen barostat (I'm then changing to Parrinello-Rahman for the production runs.)
I've tried altering time constants to no avail and was wondering if anyone had any ideas what might be causing this / places to focus my attention?
I've included my .mdp parameters below for the production run.
Many thanks,
Matthew Fisher
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000000 ; 2 * 50000000 fs = 100000 ps (100 ns)
dt = 0.002 ; 2 fs
; Output control
nstxout = 5000 ; save coordinates every 10.0 ps
nstvout = 5000 ; save velocities every 10.0 ps
nstfout = 5000 ; save forces every 10.0 ps
nstenergy = 5000 ; save energies every 10.0 ps
nstlog = 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps
compressed-x-grps = System ; save the whole system
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds 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)
rvdw = 1.0 ; short-range van der Waals 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
; 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 = 298 298 ; 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 = 5.0 ; 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
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