Hi, Could you help me with this issue? I am attempting to replicate a study involving the construction of a cyclohexane-water interface using Packmol and GROMACS. The paper describes the insertion of 1784 cyclohexane molecules into a cubic simulation box measuring 6.86×6.86×6.86 nm³. I obtained the cyclohexane structure files (.pdb and .itp) from ATB and used Packmol to create a simulation box containing 1784 cyclohexane molecules with dimensions matching those specified in the paper. However, during the energy minimization step in GROMACS, I encountered an error indicating that " The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist." How should I proceed to resolve this issue?

I am giving my minim.mdp file:

; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save 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 = 500 ; 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 = cutoff ; 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 rlist = 1.2

I have mentioned vdw cut off as 1.2 and short range electrostatic cut off as 1.2. I have tried to decrease the cut off values. still showing the same error

This is my packmol input: Since 1nm= 10 A0, I have given box size = 68.6 x 68.6 x 68.6. This is my packmol input:

cyclohexane

tolerance 2.0 filetype pdb output 8VH4_box.pdb

structure 8VH4.pdb number 1784 inside box 0. 0. 0. 68.6 68.6 68.6 end structure

Here,8VH4.pdb is the cyclohexane file which is downloaded from ATB. Could you please help me to solve the issue