DNA example lamp file

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1

Dear All,

I used the following script to run the dna example but it only writes Carbon in the dna.lmp file. Could you please help me resolving this issue? The same problem exists in the peptide example. I need all atoms printed in my *.lmp file when I use:

dump dump2 all custom 10 dna.lmp element xu yu zu

dump_modify dump2 sort id

# lammps script

# initialization
units real
dimension 3
newton on off
boundary p p p
atom_style full

# default lattice
lattice fcc 1

# pair_style
pair_style lj/charmm/coul/long 8 10 10

# angles
angle_style charmm

# bonds
bond_style harmonic

# dihedrals
dihedral_style charmm

# impropers
improper_style harmonic

# kspace
kspace_style pppm 0.0001

# read_data
read_data /Users/amirvahid/Documents/lammpsfe/examples/dna/dna/1ac7.data

# velocity
velocity all create 0 12345678 dist uniform

# processing
thermo 1
timestep 0.5

dump dump1 all atom 10 dump.xyz

# pre-run scriptlet begin
neigh_modify    delay 2 every 1
pair_modify     mix arithmetic

special_bonds   charmm

fix             2 all shake 1e-6 500 0 m 1.0 a 93

dump          dump2 all custom 10 dna.lmp element xu yu zu
dump_modify dump2 sort id
# pre-run scriptlet end

fix nve1 all nve
run 1000

Thanks!

2

Dear All,

I used the following script to run the dna example but it only writes Carbon
in the dna.lmp file. Could you please help me resolving this issue? The same
problem exists in the peptide example. I need all atoms printed in my *.lmp
file when I use:

dump dump2 all custom 10 dna.lmp element xu yu zu

dump_modify dump2 sort id

please check the documentation of the dump command, where it says:

Element is typically the chemical name of an element, which you must
assign to each type via the dump_modify element command. More
generally, it can be any string you wish to associated with an atom
type.

axel.