i get the following warnings when reruning a dcd dump file with bond_style none:
WARNING: Inconsistent image flags (src/domain.cpp:1051)
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:1172)
is it because image flags are not stored in dcd file format ?
info all
echo screen
#variable home string /home/mmurp027
variable home string /Users/mitch/Dropbox/lammps
print "HOME=${home}"
# ----- REPLICAS -----
variable pdb string 2q3z
# ----- CHARMM-GUI -----
units real
boundary p p p
newton off
pair_style lj/charmmfsw/coul/long 10 12
pair_modify mix arithmetic
#kspace_style pppm 1e-6
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmmfsw
#special_bonds charmm
improper_style harmonic
neighbor 2 bin
neigh_modify delay 5 every 1
# ----- FIXES AND DATA -----
variable dt equal 2
timestep ${dt}
fix cmap all cmap ${home}/tg2/${pdb}/lammps/charmmff.cmap
fix_modify cmap energy yes
read_data ${home}/tg2/${pdb}-min.data.gz fix cmap crossterm CMAP
#velocity all create 310.15 $((part+1)*12345) dist gaussian
read_psf ${home}/tg2/${pdb}/step3_pbcsetup.psf
include ${home}/tg2/${pdb}/lammps/restraints/constraint_angletype
#fix 1 all shake 1e-6 500 0 m 1.008 a ${constraint_angletype}
#fix 2 all npt temp 310.15 310.15 $(100.0*dt) iso 1.0 1.0 $(1000.0*dt) couple xyz mtk no pchain 0
variable prefix string "tg2-ca_20mM-partition_$(part)"
#fix 3 all colvars ${home}/tg2/tg2.colvars output ${prefix} seed $((part+1)*12345) tstat 2
# ----------- IONS -----------
group k type 46
group na type 42
group ca type 47
group mg type 43
group cl type 45
delete_atoms group k compress no
delete_atoms group na compress no
delete_atoms group mg compress no
delete_atoms random count 9 no ca NULL 12345 compress no
delete_atoms random count 1624 no cl NULL 12345 compress no
# ----- DUMP ALL EXCEPT WATER MOLECULES (PROTEIN AND IONS) -----
reset_timestep 0
group solv type 13 41
group protein_ions subtract all solv
#dump 1 protein_ions dcd 100 ${prefix}-step_$(step).dcd
# ----------- COMPUTE -----------
variable asp_glu_oc atom "(i2_psf[2]==label2type(residue,ASP)||i2_psf[2]==label2type(residue,GLU)) && type==label2type(atom,OC)"
group asp_glu_oc variable asp_glu_oc
compute 1 ca property/local patom1 patom2 group2 asp_glu_oc
compute 2 ca pair/local dist group2 asp_glu_oc
dump 1 ca local 1 tg2-oc.dump step c_1[*] c_2
dump_modify 1 header no
# ----------- RERUN -----------
pair_style zero 12 nocoeff
pair_coeff * *
bond_style none
angle_style none
dihedral_style none
improper_style none
unfix cmap
atom_modify first protein_ions
neigh_modify include protein_ions
thermo 1
thermo_style custom step spcpu cpuremain etotal temp press vol
thermo_modify lost/bond ignore
rerun /Users/mitch/Downloads/tg2-ca-1.dcd stop 3 post yes dump x y z box no format molfile dcd ./