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
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