[gmx-users] Slab shifts out of the simulation box

[Mohammed Hamza]

Dear GMX users

I'm simulating a mixture of hydrocarbons on a slab of mineral using
CHARMM27 ff. The topology of the slab was generated using the interface
forcefield script.
I see the slab shifts out of the simulation box (shown in the links below)
and get "There were 724 inconsistent shifts. Check your topology".
I check the topology and I don't see anything unusual.
Any ideas what is going on?

Thanks in advance


https://www.dropbox.com/s/hppbfa7pse6htem/final%20slab.png?dl=0
https://www.dropbox.com/s/hk3d0mrkew7c55s/initial%20box.png?dl=0

Here is the mdp that I used

; Run parameters
integrator     = md ; leap-frog integrator
nsteps     = 50000        ; 2 * 25000000 = 50000 ps
dt     = 0.001 ; 2 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
nstxout-compressed = 500
; Bond parameters
constraint_algorithm        = lincs    ; holonomic constraints
constraints             = h-bonds
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    = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw    = 1.2 ; 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 = System        ; two coupling groups - more accurate
tau_t = 0.1                ; time constant, in ps
ref_t = 350                ; reference temperature, one for each group, in K

; Periodic boundary conditions
pbc     = xyz ; 3-D PBC
periodic-molecules   = yes
; Dispersion correction
DispCorr     = no
; Velocity generation
gen_vel      = no ; Velocity generation is off