rm

mrdna/readers/list.pdf

-PSF NAMD
-
-       0 !NTITLE
-
-       7 !NATOM
-         1 0        1        DNA      DNA      D000   0.000000      150.0000 0
-         2 0        2        DNA      DNA      D001   0.000000      300.0000 0
-         3 0        3        DNA      DNA      D001   0.000000      300.0000 0
-         4 1        4        NAS      NAS      S000   0.000000      150.0000 0
-         5 1        5        NAS      NAS      S000   0.000000      150.0000 0
-         6 1        6        NAS      NAS      S001   0.000000       75.0000 0
-         7 2        7        NAS      NAS      S000   0.000000      150.0000 0
-
-       7 !NBOND
-       1       6        3       7        2       3        5       6
-       4       5        1       2        4       7 
-
-       3 !NTHETA
-       1       2       3        5       4       7        4       5       6
-
-       0 !NPHI
-
-       0 !NIMPHI
-
-
-       0 !NDON: donors
-
-
-
-       0 !NACC: acceptors
-
-
-
-       0 !NNB
-
-      0      0      0      0      0      0      0
-
-       1       0 !NGRP
-

mrdna/readers/unittest/circular.bd

-
-timestep 5e-05
-steps 100000000
-numberFluct 0                   # deprecated
-
-interparticleForce 1            # other values deprecated
-fullLongRange 0                 # deprecated
-temperature 291
-ParticleDynamicType Brown
-
-outputPeriod 10000.0
-## Energy doesn't actually get printed!
-outputEnergyPeriod 10000.0
-outputFormat dcd
-
-## Infrequent domain decomposition because this kernel is still very slow
-decompPeriod 10000
-cutoff 50
-pairlistDistance 30
-
-origin -2500.0 -2500.0 -2500.0
-systemSize 5000 5000 5000
-
-
-
-
-particle D000
-num 1
-diffusion 111.80339887498948
-gridFile potentials/null.dx
-
-particle D001
-num 2
-diffusion 79.05694150420948
-gridFile potentials/null.dx
-
-particle O000
-num 2
-diffusion 120
-gridFile potentials/null.dx
-
-particle O001
-num 1
-diffusion 79.05694150420948
-gridFile potentials/null.dx
-
-particle S000
-num 3
-diffusion 111.80339887498948
-gridFile potentials/null.dx
-
-particle S001
-num 1
-diffusion 120
-gridFile potentials/null.dx
-
-## Input coordinates
-inputParticles circular.particles.txt
-
-
-## Interaction potentials
-tabulatedPotential  1
-## The i@j@file syntax means particle type i will have NB interactions with particle type j using the potential in file
-tabulatedFile 0@0@potentials/circular-nb.D000-D000.dat
-tabulatedFile 0@1@potentials/circular-nb.D000-D001.dat
-tabulatedFile 0@2@potentials/circular-nb.D000-O000.dat
-tabulatedFile 0@3@potentials/circular-nb.D000-O001.dat
-tabulatedFile 0@4@potentials/circular-nb.D000-S000.dat
-tabulatedFile 0@5@potentials/circular-nb.D000-S001.dat
-tabulatedFile 1@1@potentials/circular-nb.D001-D001.dat
-tabulatedFile 1@2@potentials/circular-nb.D001-O000.dat
-tabulatedFile 1@3@potentials/circular-nb.D001-O001.dat
-tabulatedFile 1@4@potentials/circular-nb.D001-S000.dat
-tabulatedFile 1@5@potentials/circular-nb.D001-S001.dat
-tabulatedFile 2@2@potentials/circular-nb.O000-O000.dat
-tabulatedFile 2@3@potentials/circular-nb.O000-O001.dat
-tabulatedFile 2@4@potentials/circular-nb.O000-S000.dat
-tabulatedFile 2@5@potentials/circular-nb.O000-S001.dat
-tabulatedFile 3@3@potentials/circular-nb.O001-O001.dat
-tabulatedFile 3@4@potentials/circular-nb.O001-S000.dat
-tabulatedFile 3@5@potentials/circular-nb.O001-S001.dat
-tabulatedFile 4@4@potentials/circular-nb.S000-S000.dat
-tabulatedFile 4@5@potentials/circular-nb.S000-S001.dat
-tabulatedFile 5@5@potentials/circular-nb.S001-S001.dat
-tabulatedBondFile potentials/bond-4.000-12.000.dat
-tabulatedBondFile potentials/bond-30.000-1.500.dat
-tabulatedBondFile potentials/wlcbond-9.400-12.000.dat
-tabulatedBondFile potentials/wlcbond-6.400-12.000.dat
-tabulatedBondFile potentials/gbond-4.233-3.400.dat
-tabulatedAngleFile potentials/wlcangle-12.800-12.000.dat
-tabulatedAngleFile potentials/angle-20.882-90.000.dat
-tabulatedAngleFile potentials/angle-31.289-180.000.dat
-tabulatedDihedralFile potentials/dihedral-76.537-34.483.dat
-tabulatedDihedralFile potentials/dihedral-10.430-180.000.dat
-tabulatedDihedralFile potentials/dihedral-21.531--120.000.dat
-tabulatedDihedralFile potentials/dihedral-21.531-120.000.dat
-inputBonds potentials/circular.bonds.txt
-inputAngles potentials/circular.angles.txt
-inputDihedrals potentials/circular.dihedrals.txt
-inputExcludes potentials/circular.exculsions.txt

mrdna/readers/unittest/circular.particles.txt

-ATOM 0 D000 0.500000 0.000000 5.100000
-ATOM 1 O000 1.932597 -0.444597 5.100000
-ATOM 2 D001 0.500000 0.000000 11.900000
-ATOM 3 O001 1.932597 0.444597 11.900000
-ATOM 4 D001 0.500000 0.000000 18.700000
-ATOM 5 O000 1.429173 1.177556 18.700000
-ATOM 6 S000 0.000000 0.000000 -1.700000
-ATOM 7 S000 0.000000 0.000000 1.700000
-ATOM 8 S001 0.000000 0.000000 5.100000
-ATOM 9 S000 0.000000 0.000000 20.400000

mrdna/readers/unittest/circular.pdb

-CRYST1 5000.000 5000.000 5000.000  90.00  90.00  90.00 P 1           1
-ATOM      1 DNA  DNA A 1       0.50000 0.00000 5.10000  0.00  0.00   0     0
-ATOM      2  O   O   A 2       1.93259-0.44459 5.10000  0.00  0.00   0     0
-ATOM      3 DNA  DNA A 3       0.50000 0.00000 11.9000  0.00  0.00   0     0
-ATOM      4  O   O   A 4       1.93259 0.44459 11.9000  0.00  0.00   0     0
-ATOM      5 DNA  DNA A 5       0.50000 0.00000 18.7000  0.00  0.00   0     0
-ATOM      6  O   O   A 6       1.42917 1.17755 18.7000  0.00  0.00   0     0
-ATOM      7 NAS  NAS A 7       0.00000 0.00000-1.70000  0.00  0.00   0     1
-ATOM      8 NAS  NAS A 8       0.00000 0.00000 1.70000  0.00  0.00   0     1
-ATOM      9 NAS  NAS A 9       0.00000 0.00000 5.10000  0.00  0.00   0     1
-ATOM     10 NAS  NAS A 10      0.00000 0.00000 20.4000  0.00  0.00   0     2

mrdna/readers/unittest/circular.psf

-PSF NAMD
-
-       0 !NTITLE
-
-      10 !NATOM
-         1 0        1        DNA      DNA      D000   0.000000      150.0000 0
-         2 0        2        O        O        O000   0.000000        0.0000 0
-         3 0        3        DNA      DNA      D001   0.000000      300.0000 0
-         4 0        4        O        O        O001   0.000000      300.0000 0
-         5 0        5        DNA      DNA      D001   0.000000      300.0000 0
-         6 0        6        O        O        O000   0.000000        0.0000 0
-         7 1        7        NAS      NAS      S000   0.000000      150.0000 0
-         8 1        8        NAS      NAS      S000   0.000000      150.0000 0
-         9 1        9        NAS      NAS      S001   0.000000       75.0000 0
-        10 2        10       NAS      NAS      S000   0.000000      150.0000 0
-
-      10 !NBOND
-       3       5        5      10        1       2        8       9
-       7      10        7       8        1       9        3       4
-       1       3        5       6 
-
-       7 !NTHETA
-       1       3       5        8       7      10        4       3       5
-       3       5       6        2       1       3        1       3       4
-       7       8       9 
-
-       5 !NPHI
-       1       3       4       5       10       5       3       6
-       2       1       3       4        4       3       5       6
-       9       1       3       2 
-
-       0 !NIMPHI
-
-
-       0 !NDON: donors
-
-
-
-       0 !NACC: acceptors
-
-
-
-       0 !NNB
-
-      0       0       0       0       0       0       0       0
-      0      0
-
-       1       0 !NGRP
-