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

[Justin Lemkul]

On 3/12/18 3:26 PM, SHYANTANI MAITI wrote:
> 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.
>

Probably a PBC issue. Use trjconv to re-center everything before 
computing RMSD.

-Justin

> 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
>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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