Dear,
First, I will give my thanks to Ahmed E. Ismail and Arnab who help me deal with my question. But the question remains . I have used ewald and pppm to compute coul interaction. the code is attached in the bottom. When I use ewald, it can run normally. But when I use pppm, it gives me some error notice.
I have taked Arnab and AEI 's advice and minimized the system . But it is useless . Who would like to give me more suggestion . I believe that the kspace_modify command is helpful. I have tried to change the simulation box, when the box’s size is shorter than 240 (-120.0005—120.0005 in each dimension),
it can work normally though without modify command .But if it’s longer, It can’t work whatever the modify command parameter It’s.
I hope someone give me a hand. Thanks in advance.
when I use kspace_style pppm, it give a error
G vector = nan
grid = 0 0 0
RMS precision = nan
ERROR: PPPM stencil extends too far, reduce PPPM order
When I use kspace_style pppm and modify, it give a error
PPPM initialization …
G vector = nan
grid = 50 50 50
RMS precision = nan
brick FFT buffer size/proc = 41552 32500 8904
Setting up run …
Memory usage per processor = 12.9462 Mbytes
Step Temp PotEng KinEng TotEng E_coul E_pair E_bond
0 26.026281 nan 38.876757 nan nan nan 13.440813
ERROR: Out of range atoms - cannot compute PPPM
Wende Tian
CODE:
dimension 3
boundary p p p
units lj
neighbor 0.3 bin
neigh_modify every 1 delay 5 check yes
atom_style full
bond_style harmonic
special_bonds 0.0 1.0 1.0
angle_style harmonic
Soft peotential push-off
read_data data.dna
group polymer type 1
group ion type 2
velocity all create 2.0 1112345
bond_coeff 1 3968.5 1.2246
angle_coeff 1 70 180
pair_style soft 2.5
pair_coeff * * 1.0 60.0
fix 1 all nve
fix 2 all langevin 2.0 1.5 1000 699443
thermo 500
dump 1 all atom 100 dump1.project
run 5000
#Main run
#The cutoff distances are changeable here to different affinities between atoms
#minimize 1.0e-4 1000 15000
timestep 0.0005
pair_style hybrid/overlay lj/expand 2.0 coul/long 10.0
pair_coeff 1 1 lj/expand 1.0 1.12246 0.0 1.5
pair_coeff 1 2 lj/expand 1.0 0.98 0.0 1.2
pair_coeff 2 2 lj/expand 1.0 0.6735 0.0 0.825
pair_coeff * * coul/long
dielectric 80.0
pair_modify shift yes
#minimize 1.0e-4 1000 15000
kspace_style pppm 0.0001 # ewald 0.0001
kspace_modify mesh 50 50 50 order 2 # use or not use
fix 5 all langevin 1.5 1.2 1000 699447
#minimize 1.0e-4 1000 15000
thermo 100
thermo_style custom step temp pe ke etotal ecoul epair ebond
dump 2 polymer atom 1000 dump.polymer.project
dump 3 ion atom 1000 dump.ion.project
dump 4 all atom 1000 dump.project
restart 5000 restart.%.dna
reset_timestep 0
run 50000