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in.chromosome
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in.chromosome
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variable rseed equal 4928459
# ---- Settings ----
variable hT equal 3.0
variable T equal 1.0
units lj
atom_style full
bond_style class2
boundary s s s
special_bonds lj 0.0 0.0 1.0 extra 512
read_data ../../../../inputFiles/lmps_input/Gm12878/data.chromosome.chr1
neighbor 0.4 bin
neigh_modify every 1 delay 1
atom_modify sort 0 0.0
# ---- Force Field ----
bond_coeff 1 2.0 20.0 20.0 20.0
angle_style cosine
angle_coeff 1 2.0
# ---- Energy funtion ----
pair_style hybrid/overlay table linear 10000 tanhlr/cut/ideala 6.0 0 15 /nobackup1b/users/qiyf/project_3d_genome/swf-Dragon-extension-release/runMolecularDynamics/../src/md/lmps_input//ucs_chrom.txt /nobackup1b/users/qiyf/project_3d_genome/swf-Dragon-extension-release/runMolecularDynamics/inputFiles/epig_input/chromStates/Gm12878/Gm12878_chr1_chromatin_states_From20MbTo45Mb.txt tanhlr/cut/ideal 6.0 /nobackup1b/users/qiyf/project_3d_genome/swf-Dragon-extension-release/runMolecularDynamics/../src/md/lmps_input//uctcf_chrom.txt /nobackup1b/users/qiyf/project_3d_genome/swf-Dragon-extension-release/runMolecularDynamics/inputFiles/epig_input/ctcfSites/Gm12878/Gm12878_chr1_ctcf_index_From20MbTo45Mb.txt 4
pair_coeff * * table /nobackup1b/users/qiyf/project_3d_genome/swf-Dragon-extension-release/runMolecularDynamics/../src/md/lmps_input//soft_core_lj_4kT.table soft_core_lj 1.12
pair_coeff * * tanhlr/cut/ideal 0.0 1.76 3.72
pair_coeff * * tanhlr/cut/ideala 0.0 1.76 3.72
pair_modify tabinner 0.0000000001 shift yes
thermo 10000
thermo_style custom time temp pe etotal epair ebond eangle press vol
thermo_modify norm no flush yes
# ---- Spherical confinement ----
region nucleus sphere 0.0 0.0 0.0 26.56193 side in
fix wall all wall/region nucleus lj126 1.0 1.0 1.12
# ---- Minimization ----
minimize 1.0e-4 1.0e-6 100 1000
# ---- Energy and velocity ----
fix 1 all nve
velocity all create ${hT} ${rseed} rot yes mom yes dist gaussian
# ---- High temperature equilibration ----
#dump 1 all dcd 2000 DUMP_FILE_highT.dcd
#dump_modify 1 unwrap yes
#timestep 0.006
#fix 2 all langevin ${hT} ${T} 0.5 ${rseed}
#run 4000000
# ---- Normal temperature ----
#undump 1
#unfix 2
dump 2 all dcd 2000 DUMP_FILE.dcd
dump_modify 2 unwrap yes
timestep 0.012
fix 3 all langevin ${T} ${T} 0.5 ${rseed}
run 40000000