[lammps-users] about special_bonds

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1

Dear,

I can’t completely understand the manual about special_bonds command.

The 1st coefficient is the weighting factor on 1−2 atom pairs, which
are those directly bonded to each other. The 2nd coefficient is the weighting factor on 1−3 atom pairs which are those separated by 2 bonds (e.g. the 2 H atoms in a water molecule). The 3rd coefficient is the weighting factor on 1−4 atom pairs which are separated by 3 bonds (e.g. the 1st and 4th atoms in a dihedral interaction).

What is the difference between 0.0 and 1.0? When two or three atoms are considered in one bond, what does the force distribute in deed. Who can give me some examples in detail?
for example

O when I give para 0.0 1.0 1.0 or 1.0 0.0 1.0 ,what does it mean
/
/ \ C====O
H H

please give me a hand on this, appreciate your kind help!. Thanks

Wende Tian

2

Dear Wende,

The factors indicate what is the scaling factor for the pair (nonbond) interaction between toms that are 1, 2 or 3
bonds apart.

Using water as an example:

-if you use the option 0.0 1.0 1.0 it will consider both the angle interaction H-O-H and 100% of the
pair interaction (e.g. LJ) between H and H of the same molecule.

-If you select 1.0 0.0 1.0, then you will have 100% of the pair interaction between atoms that are bonded (O-H)
besides the bond interaction between them. In this case the H and H of each water molecule will only interact
through the angle term.

Published force fields always specify the values of these coefficients; look in the paper of the force field you use
to select the right values. The standard is 0 for atoms that are 1 and 2 bonds apart; the value for atoms 3 bonds
apart is very specific for each potential.
vale

3

Dear,

When I run the following code(in blue) with LAMMPS, system give me a error notice(in red)
“Out of range atoms - cannot compute PPPM”, manual says that One or more atoms are attempting to map their charge to a PPPM grid point that is not owned by a processor. This is usually because an atom has moved to far in a single timestep.

But I don’t know how solve it with kspace_modify command. my simulation box is 250 ppp.
How can I deal with some question like this? I hope somebody give me some adivce. Thanks in advance.

LAMMPS (5 Oct 2007)
…

read_data data.dna
Scanning data file …
1 = max bonds/atom
1 = max angles/atom
Reading data file …
orthogonal box = (-123.311 -123.311 -123.311) to (123.311 123.311 123.311)
1 by 1 by 2 processor grid
240 atoms
179 bonds
178 angles
Finding 1-2 1-3 1-4 neighbors …
2 = max # of 1-2 neighbors
2 = max # of special neighbors

…

restart 5000 restart.%.dna
reset_timestep 0
run 4PPPM initialization …
G vector = nan
grid = 48 48 60
RMS precision = nan
brick FFT buffer size/proc = 85833 69120 15606
Setting up run …
Memory usage per processor = 96.3655 Mbytes
Step Temp PotEng KinEng TotEng E_coul E_pair E_bond
0 23.980464 nan 35.820819 nan nan nan 12.25924
ERROR: Out of range atoms - cannot compute PPPM

echo screen
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 30.0 1.12246

fix 1 all nve
fix 2 all langevin 2.0 1.5 1000 699443

thermo 500

dump 1 all atom 100 dump1.project

run 10000

#Main run
#The cutoff distances are changeable here to different affinities between atoms

timestep 0.001

pair_style hybrid/overlay lj/expand 1.12246 coul/long 10.0
pair_coeff 1 1 lj/expand 1.0 1.12246 0.0 1.2246
pair_coeff 1 2 lj/expand 1.0 0.98 0.0 0.98
pair_coeff 2 2 lj/expand 1.0 0.6735 0.0 0.6735
pair_coeff * * coul/long
dielectric 80.0
pair_modify shift yes

kspace_style pppm 0.0001
kspace_modify mesh 24 24 30 order 6

fix 5 all langevin 1.5 1.2 1000 699447

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