生成h2o-out.pdb 文件，部分内容如下：
HEADER
TITLE Built with Packmol
REMARK Packmol generated pdb file
REMARK Home-Page: http://m3g.iqm.unicamp.br/packmol
REMARK
HETATM 1 O SOL A 1 -3.286 -9.267 -0.230 1.00 0.00 O
HETATM 2 H SOL A9999 -2.832 -10.000 0.215 1.00 0.00 H
HETATM 3 H SOL A9999 -4.189 -9.187 0.119 1.00 0.00 H
mdp文件如下：
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 = 200000 ; 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 = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
但是当我gmx grompp -f minim.mdp -o energy-minimization.tpr -c h2o-out.pdb时，我得到以下报错信息：
ERROR 1 [file topol.top, line 12]:
ERROR: 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.