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rename CG-DNA potential files

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This commit is contained in:
Axel Kohlmeyer
2024-06-20 14:33:26 -04:00
parent 00d7aa935f
commit 734fdf4a46
25 changed files with 461 additions and 319 deletions
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16
examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/in.duplex1
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@ -26,18 +26,18 @@ group all type 1 4
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * oxdna.lj
bond_coeff * oxdna_lj.cgdna
special_bonds lj 0 1 1
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv oxdna.lj
pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 oxdna.lj
pair_coeff * * oxdna/hbond seqav oxdna.lj
pair_coeff 1 4 oxdna/hbond seqav oxdna.lj
pair_coeff 2 3 oxdna/hbond seqav oxdna.lj
pair_coeff * * oxdna/xstk oxdna.lj
pair_coeff * * oxdna/coaxstk oxdna.lj
pair_coeff * * oxdna/excv oxdna_lj.cgdna
pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 oxdna_lj.cgdna
pair_coeff * * oxdna/hbond seqav oxdna_lj.cgdna
pair_coeff 1 4 oxdna/hbond seqav oxdna_lj.cgdna
pair_coeff 2 3 oxdna/hbond seqav oxdna_lj.cgdna
pair_coeff * * oxdna/xstk oxdna_lj.cgdna
pair_coeff * * oxdna/coaxstk oxdna_lj.cgdna
# NVE ensemble
fix 1 all nve/asphere

1
examples/PACKAGES/cgdna/examples/lj_units/oxDNA/potential_file/oxdna_lj.cgdna Symbolic link
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@ -0,0 +1 @@
../../../../../../../potentials/oxdna_lj.cgdna

24
examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/in.duplex1
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@ -1,6 +1,6 @@
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 0.1
variable rhos equal 0.2
@ -27,19 +27,19 @@ group all type 1 4
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * oxdna2.lj
bond_coeff * oxdna2_lj.cgdna
special_bonds lj 0 1 1
# oxDNA2 pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv oxdna2.lj
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2.lj
pair_coeff * * oxdna2/hbond seqdep oxdna2.lj
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2.lj
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2.lj
pair_coeff * * oxdna2/xstk oxdna2.lj
pair_coeff * * oxdna2/coaxstk oxdna2.lj
pair_coeff * * oxdna2/dh 0.1 0.5 oxdna2.lj
pair_coeff * * oxdna2/excv oxdna2_lj.cgdna
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2_lj.cgdna
pair_coeff * * oxdna2/hbond seqdep oxdna2_lj.cgdna
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2_lj.cgdna
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2_lj.cgdna
pair_coeff * * oxdna2/xstk oxdna2_lj.cgdna
pair_coeff * * oxdna2/coaxstk oxdna2_lj.cgdna
pair_coeff * * oxdna2/dh 0.1 0.5 oxdna2_lj.cgdna
# NVE ensemble
fix 1 all nve/asphere

1
examples/PACKAGES/cgdna/examples/lj_units/oxDNA2/potential_file/oxdna2_lj.cgdna Symbolic link
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@ -0,0 +1 @@
../../../../../../../potentials/oxdna2_lj.cgdna

26
examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/in.duplex2
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@ -1,6 +1,6 @@
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 0.1
variable rhos equal 0.5
@ -27,20 +27,20 @@ group all type 1 4
# oxRNA2 bond interactions - FENE backbone
bond_style oxrna2/fene
bond_coeff * oxrna2.lj
bond_coeff * oxrna2_lj.cgdna
special_bonds lj 0 1 1
# oxRNA2 pair interactions
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
pair_coeff * * oxrna2/excv oxrna2.lj
pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2.lj
pair_coeff * * oxrna2/hbond seqdep oxrna2.lj
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2.lj
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2.lj
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.lj
pair_coeff * * oxrna2/xstk oxrna2.lj
pair_coeff * * oxrna2/coaxstk oxrna2.lj
pair_coeff * * oxrna2/dh 0.1 0.5 oxrna2.lj
pair_coeff * * oxrna2/excv oxrna2_lj.cgdna
pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2_lj.cgdna
pair_coeff * * oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_lj.cgdna
pair_coeff * * oxrna2/xstk oxrna2_lj.cgdna
pair_coeff * * oxrna2/coaxstk oxrna2_lj.cgdna
pair_coeff * * oxrna2/dh 0.1 0.5 oxrna2_lj.cgdna
# NVE ensemble
fix 1 all nve/asphere

1
examples/PACKAGES/cgdna/examples/lj_units/oxRNA2/potential_file/oxrna2_lj.cgdna Symbolic link
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@ -0,0 +1 @@
../../../../../../../potentials/oxrna2_lj.cgdna

22
examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/in.duplex1
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@ -1,7 +1,7 @@
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 300.0
units real
@ -27,18 +27,18 @@ group all type 1 4
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * oxdna.real
bond_coeff * oxdna_real.cgdna
special_bonds lj 0 1 1
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv oxdna.real
pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 oxdna.real
pair_coeff * * oxdna/hbond seqav oxdna.real
pair_coeff 1 4 oxdna/hbond seqav oxdna.real
pair_coeff 2 3 oxdna/hbond seqav oxdna.real
pair_coeff * * oxdna/xstk oxdna.real
pair_coeff * * oxdna/coaxstk oxdna.real
pair_coeff * * oxdna/excv oxdna_real.cgdna
pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 oxdna_real.cgdna
pair_coeff * * oxdna/hbond seqav oxdna_real.cgdna
pair_coeff 1 4 oxdna/hbond seqav oxdna_real.cgdna
pair_coeff 2 3 oxdna/hbond seqav oxdna_real.cgdna
pair_coeff * * oxdna/xstk oxdna_real.cgdna
pair_coeff * * oxdna/coaxstk oxdna_real.cgdna
# NVE ensemble
fix 1 all nve/asphere

1
examples/PACKAGES/cgdna/examples/real_units/oxDNA/potential_file/oxdna_real.cgdna Symbolic link
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@ -0,0 +1 @@
../../../../../../../potentials/oxdna_real.cgdna

24
examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/in.duplex1
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@ -1,7 +1,7 @@
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 300.0
variable rhos equal 0.2
@ -28,19 +28,19 @@ group all type 1 4
# oxDNA2 bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * oxdna2.real
bond_coeff * oxdna2_real.cgdna
special_bonds fene
# oxDNA2 pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv oxdna2.real
pair_coeff * * oxdna2/stk seqav 300.0 8.06199211612242 0.005309213 oxdna2.real
pair_coeff * * oxdna2/hbond seqav oxdna2.real
pair_coeff 1 4 oxdna2/hbond seqav oxdna2.real
pair_coeff 2 3 oxdna2/hbond seqav oxdna2.real
pair_coeff * * oxdna2/xstk oxdna2.real
pair_coeff * * oxdna2/coaxstk oxdna2.real
pair_coeff * * oxdna2/dh 300.0 0.5 oxdna2.real
pair_coeff * * oxdna2/excv oxdna2_real.cgdna
pair_coeff * * oxdna2/stk seqav 300.0 8.06199211612242 0.005309213 oxdna2_real.cgdna
pair_coeff * * oxdna2/hbond seqav oxdna2_real.cgdna
pair_coeff 1 4 oxdna2/hbond seqav oxdna2_real.cgdna
pair_coeff 2 3 oxdna2/hbond seqav oxdna2_real.cgdna
pair_coeff * * oxdna2/xstk oxdna2_real.cgdna
pair_coeff * * oxdna2/coaxstk oxdna2_real.cgdna
pair_coeff * * oxdna2/dh 300.0 0.5 oxdna2_real.cgdna
# NVE ensemble

1
examples/PACKAGES/cgdna/examples/real_units/oxDNA2/potential_file/oxdna2_real.cgdna Symbolic link
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@ -0,0 +1 @@
../../../../../../../potentials/oxdna2_real.cgdna

26
examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/in.duplex2
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@ -1,7 +1,7 @@
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
variable T equal 300.0
variable rhos equal 0.5
@ -28,20 +28,20 @@ group all type 1 4
# oxRNA2 bond interactions - FENE backbone
bond_style oxrna2/fene
bond_coeff * oxrna2.real
bond_coeff * oxrna2_real.cgdna
special_bonds lj 0 1 1
# oxRNA2 pair interactions
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
pair_coeff * * oxrna2/excv oxrna2.real
pair_coeff * * oxrna2/stk seqdep 300.0 8.35864576375849 0.005504556 oxrna2.real
pair_coeff * * oxrna2/hbond seqdep oxrna2.real
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2.real
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2.real
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.real
pair_coeff * * oxrna2/xstk oxrna2.real
pair_coeff * * oxrna2/coaxstk oxrna2.real
pair_coeff * * oxrna2/dh 300.0 0.5 oxrna2.real
pair_coeff * * oxrna2/excv oxrna2_real.cgdna
pair_coeff * * oxrna2/stk seqdep 300.0 8.35864576375849 0.005504556 oxrna2_real.cgdna
pair_coeff * * oxrna2/hbond seqdep oxrna2_real.cgdna
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2_real.cgdna
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2_real.cgdna
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2_real.cgdna
pair_coeff * * oxrna2/xstk oxrna2_real.cgdna
pair_coeff * * oxrna2/coaxstk oxrna2_real.cgdna
pair_coeff * * oxrna2/dh 300.0 0.5 oxrna2_real.cgdna
# NVE ensemble
fix 1 all nve/asphere

1
examples/PACKAGES/cgdna/examples/real_units/oxRNA2/potential_file/oxrna2_real.cgdna Symbolic link
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@ -0,0 +1 @@
../../../../../../../potentials/oxrna2_real.cgdna