[gmx-users] Solid surface simulation and PBC issues

[Samuel Asante Afari]

Dear Users,
I am trying to simulate kaolinite in explicit water. After building my structure, I try to minimize it but I tend to get very high positive potential energy. After doing some research, one possible explanation is the broken bonds across the periodic boundary, which I notice in my surface model when I view in VMD. I have tried all that I can to fix it i.e using trjconv, whole, nojump, mol sequence and also adjusting box size. My question is, is the high potential energy caused by the broken bonds? Is this problem fixable by trjconv or it is a matter of topology? Which part of the topology cause this issue? Any suggestions to help me fix it?

Thank you in advance

Sam

Please see attached my em.mdp and energy output.  Also attached is a picture of the structure with broken bonds.

integrator  = steep         ; Algorithm (steep = steepest descent minimization)
emtol       = 1000.0        ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep      = 0.01          ; Minimization step size
nsteps      = 50000         ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist         = 1         ; Frequency to update the neighbor list and long range forces
cutoff-scheme   = Verlet    ; Buffered neighbor searching
ns_type         = grid      ; Method to determine neighbor list (simple, grid)
coulombtype     = PME       ; Treatment of long range electrostatic interactions
rcoulomb        = 1.2       ; Short-range electrostatic cut-off
rvdw            = 1.2       ; Short-range Van der Waals cut-off
pbc             = xyz       ; Periodic Boundary Conditions in all 3 dimensions
periodic_molecules = yes



Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 19 steps
Potential Energy  =  7.0229306e+05
Maximum force     =  9.4779437e+02 on atom 522
Norm of force     =  5.7396594e+02