[gmx-users] Sudden increase in RMSD values for 100ns simulation of protein-protein complex

[SHYANTANI MAITI]

Dear all,
I have been simulating a protein-protein complex using gromacs for 100ns.
after the completion of job, I find that the rmsd values have undergone a
sudden increase after 20ns of the simulation. Is my simulation going wrong
somewhere? Can protein-protein complexes be simulated in gromacs?
Following is the final mdp file for simulating my protein-protein complex.


title        = MD simulation
; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 50000000    ; 2 * 50000000 = 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
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
                                ; nstxout-compressed replaces nstxtcout
compressed-x-grps   = System    ; replaces xtc-grps
; Bond parameters
continuation            = yes        ; Restarting after NPT
constraint_algorithm    = lincs        ; holonomic constraints
constraints                = all-bonds    ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter                = 1            ; accuracy of LINCS
lincs_order                = 4            ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
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        = 300       300            ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl                = Berendsen        ; 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



-- 
Best regards,
*Shyantani Maiti*