[gmx-users] Solid surface simulation and PBC issues

[Benson Muite]

On 10/11/19 6:41 PM, Samuel Asante Afari wrote:
> 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?
Picture not attached. May want to post it online somewhere and put a 
link to it. It is not clear why you have broken bonds across the 
periodic boundary. What is you initial setup? Should kaolinite be at a 
low concentration? Are you able to use a bigger periodic box?
>
> 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
>