forked from lijiext/lammps
Verified oxDNA with modified nucleotide layout
This commit is contained in:
Oliver Henrich
parent
7a75cd111c
commit
7435084375
Binary file not shown.
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@ -1,74 +0,0 @@
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# LAMMPS data file
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10 atoms
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10 ellipsoids
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8 bonds
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4 atom types
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1 bond types
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# System size
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-20.000000 20.000000 xlo xhi
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-20.000000 20.000000 ylo yhi
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-20.000000 20.000000 zlo zhi
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# Atom masses for each atom type
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Masses
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1 3.1575
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2 3.1575
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3 3.1575
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4 3.1575
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# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
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Atoms
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1 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 1 1 1
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2 1 1.3274493266864451e-01 -4.2912827978022683e-01 3.7506163469402809e-01 1 1 1
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3 1 4.8460810659772807e-01 -7.0834970533509178e-01 7.5012326938805618e-01 1 1 1
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4 1 9.3267359196674593e-01 -7.4012419946742802e-01 1.1251849040820843e+00 1 1 1
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5 1 1.3204192238113461e+00 -5.1335201721887447e-01 1.5002465387761124e+00 1 1 1
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6 4 1.9958077618865377e-01 5.1335201721887447e-01 1.5002465387761124e+00 1 1 1
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7 4 5.8732640803325409e-01 7.4012419946742802e-01 1.1251849040820843e+00 1 1 1
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8 4 1.0353918934022719e+00 7.0834970533509178e-01 7.5012326938805618e-01 1 1 1
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9 4 1.3872550673313555e+00 4.2912827978022683e-01 3.7506163469402809e-01 1 1 1
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10 4 1.5200000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 1 1 1
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# Atom-ID, translational, rotational velocity
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Velocities
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1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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# Atom-ID, shape, quaternion
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Ellipsoids
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1 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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2 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 9.5533648912560598e-01 0.0000000000000000e+00 0.0000000000000000e+00 2.9552020666133955e-01
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3 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 8.2533561490967822e-01 0.0000000000000000e+00 0.0000000000000000e+00 5.6464247339503526e-01
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4 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 6.2160996827066439e-01 0.0000000000000000e+00 0.0000000000000000e+00 7.8332690962748319e-01
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5 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 3.6235775447667351e-01 0.0000000000000000e+00 0.0000000000000000e+00 9.3203908596722607e-01
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6 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 9.3203908596722607e-01 -3.6235775447667351e-01 0.0000000000000000e+00
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7 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 7.8332690962748319e-01 -6.2160996827066439e-01 0.0000000000000000e+00
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8 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 5.6464247339503526e-01 -8.2533561490967822e-01 0.0000000000000000e+00
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9 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 2.9552020666133955e-01 -9.5533648912560598e-01 0.0000000000000000e+00
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10 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00
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# Bond topology
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Bonds
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1 1 1 2
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2 1 2 3
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3 1 3 4
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4 1 4 5
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5 1 6 7
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6 1 7 8
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7 1 8 9
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8 1 9 10
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
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@ -1,97 +0,0 @@
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# LAMMPS data file
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16 atoms
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16 ellipsoids
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13 bonds
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4 atom types
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1 bond types
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# System size
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-20.0 20.0 xlo xhi
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-20.0 20.0 ylo yhi
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-20.0 20.0 zlo zhi
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# Atom masses for each atom type
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Masses
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1 3.1575
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2 3.1575
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3 3.1575
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4 3.1575
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# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
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Atoms
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1 1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1 1 1
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2 1 1.327449326686445e-01 -4.291282797802268e-01 3.750616346940281e-01 1 1 1
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3 1 4.846081065977281e-01 -7.083497053350921e-01 7.501232693880562e-01 1 1 1
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4 1 9.326735919667459e-01 -7.401241994674285e-01 1.125184904082084e+00 1 1 1
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5 1 1.320419223811347e+00 -5.133520172188747e-01 1.500246538776112e+00 1 1 1
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6 1 1.512394297416339e+00 -1.072512061254991e-01 1.875308173470140e+00 1 1 1
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7 1 1.441536396413952e+00 3.363155369040876e-01 2.250369808164169e+00 1 1 1
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8 1 1.132598224218932e+00 6.623975870343269e-01 2.625431442858197e+00 1 1 1
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9 4 5.873264080332541e-01 7.401241994674285e-01 1.125184904082084e+00 1 1 1
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10 4 1.035391893402272e+00 7.083497053350921e-01 7.501232693880562e-01 1 1 1
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11 4 1.387255067331356e+00 4.291282797802267e-01 3.750616346940281e-01 1 1 1
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12 4 1.520000000000000e+00 1.260981291332700e-33 0.000000000000000e+00 1 1 1
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13 4 3.874017757810680e-01 -6.623975870343268e-01 2.625431442858197e+00 1 1 1
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14 4 7.846360358604798e-02 -3.363155369040874e-01 2.250369808164169e+00 1 1 1
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15 4 7.605702583661333e-03 1.072512061254995e-01 1.875308173470140e+00 1 1 1
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16 4 1.995807761886533e-01 5.133520172188748e-01 1.500246538776112e+00 1 1 1
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# Atom-ID, translational, rotational velocity
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Velocities
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1 0.0 0.0 0.0 0.0 0.0 0.0
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2 0.0 0.0 0.0 0.0 0.0 0.0
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3 0.0 0.0 0.0 0.0 0.0 0.0
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4 0.0 0.0 0.0 0.0 0.0 0.0
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5 0.0 0.0 0.0 0.0 0.0 0.0
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6 0.0 0.0 0.0 0.0 0.0 0.0
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7 0.0 0.0 0.0 0.0 0.0 0.0
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8 0.0 0.0 0.0 0.0 0.0 0.0
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9 0.0 0.0 0.0 0.0 0.0 0.0
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10 0.0 0.0 0.0 0.0 0.0 0.0
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11 0.0 0.0 0.0 0.0 0.0 0.0
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12 0.0 0.0 0.0 0.0 0.0 0.0
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13 0.0 0.0 0.0 0.0 0.0 0.0
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14 0.0 0.0 0.0 0.0 0.0 0.0
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15 0.0 0.0 0.0 0.0 0.0 0.0
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16 0.0 0.0 0.0 0.0 0.0 0.0
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# Atom-ID, shape, quaternion
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Ellipsoids
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1 1.1739845031423408 1.1739845031423408 1.1739845031423408 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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2 1.1739845031423408 1.1739845031423408 1.1739845031423408 9.553364891256060e-01 0.000000000000000e+00 0.000000000000000e+00 2.955202066613395e-01
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3 1.1739845031423408 1.1739845031423408 1.1739845031423408 8.253356149096783e-01 0.000000000000000e+00 0.000000000000000e+00 5.646424733950354e-01
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4 1.1739845031423408 1.1739845031423408 1.1739845031423408 6.216099682706646e-01 0.000000000000000e+00 0.000000000000000e+00 7.833269096274833e-01
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5 1.1739845031423408 1.1739845031423408 1.1739845031423408 3.623577544766736e-01 0.000000000000000e+00 0.000000000000000e+00 9.320390859672263e-01
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6 1.1739845031423408 1.1739845031423408 1.1739845031423408 7.073720166770291e-02 0.000000000000000e+00 0.000000000000000e+00 9.974949866040544e-01
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7 1.1739845031423408 1.1739845031423408 1.1739845031423408 -2.272020946930869e-01 -0.000000000000000e+00 0.000000000000000e+00 9.738476308781953e-01
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8 1.1739845031423408 1.1739845031423408 1.1739845031423408 -5.048461045998575e-01 -0.000000000000000e+00 0.000000000000000e+00 8.632093666488738e-01
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9 1.1739845031423408 1.1739845031423408 1.1739845031423408 4.796493962806427e-17 7.833269096274833e-01 -6.216099682706646e-01 3.806263289803786e-17
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10 1.1739845031423408 1.1739845031423408 1.1739845031423408 5.707093416549944e-17 5.646424733950354e-01 -8.253356149096784e-01 2.218801320830406e-17
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11 1.1739845031423408 1.1739845031423408 1.1739845031423408 6.107895212550935e-17 2.955202066613394e-01 -9.553364891256061e-01 4.331404380149668e-18
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12 1.1739845031423408 1.1739845031423408 1.1739845031423408 5.963096920061075e-17 0.000000000000000e+00 -1.000000000000000e+00 -1.391211590127312e-17
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13 1.1739845031423408 1.1739845031423408 1.1739845031423408 5.285632939302787e-17 8.632093666488739e-01 5.048461045998572e-01 -3.091290830301125e-17
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14 1.1739845031423408 1.1739845031423408 1.1739845031423408 4.136019110019290e-17 9.738476308781953e-01 2.272020946930868e-01 -4.515234267244800e-17
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15 1.1739845031423408 1.1739845031423408 1.1739845031423408 2.616947011741696e-17 9.974949866040544e-01 -7.073720166770313e-02 -5.535845274597425e-17
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16 1.1739845031423408 1.1739845031423408 1.1739845031423408 8.641108308308281e-18 9.320390859672264e-01 -3.623577544766736e-01 -6.061955710708163e-17
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# Bond-ID, type, atom pairs
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Bonds
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1 1 1 2
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2 1 2 3
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3 1 3 4
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4 1 4 5
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5 1 5 6
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6 1 6 7
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7 1 7 8
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8 1 13 14
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9 1 14 15
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10 1 15 16
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11 1 9 10
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12 1 10 11
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13 1 11 12
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,73 @@
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# LAMMPS data file
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10 atoms
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10 ellipsoids
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8 bonds
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4 atom types
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1 bond types
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# System size
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-20.000000 20.000000 xlo xhi
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-20.000000 20.000000 ylo yhi
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-20.000000 20.000000 zlo zhi
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Masses
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1 3.1575
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2 3.1575
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3 3.1575
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4 3.1575
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# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
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Atoms
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1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
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2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
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3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
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4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
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5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
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6 4 -4.829362784135484e-01 3.560513319622209e-01 1.559051420521249e+00 2 1 1
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7 1 -1.824198365552941e-01 5.715968887521516e-01 1.169288565390937e+00 2 1 1
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8 2 1.874009511073395e-01 5.699832309147913e-01 7.795257102606243e-01 2 1 1
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9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
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10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
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# Atom-ID, translational, rotational velocity
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Velocities
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1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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# Atom-ID, shape, quaternion
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Ellipsoids
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1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
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3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
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4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
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5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
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6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00
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7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847401e-01 -5.899012371043604e-01 0.000000000000000e+00
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8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357896e-01 -8.100416404457959e-01 0.000000000000000e+00
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9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252947e-01 0.000000000000000e+00
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10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.110223024625157e-16 1.000000000000000e+00 -0.000000000000000e+00
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# Bond topology
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Bonds
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1 1 1 2
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2 1 2 3
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3 1 3 4
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4 1 4 5
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5 1 6 7
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6 1 7 8
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7 1 8 9
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8 1 9 10
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@ -24,18 +24,18 @@ set atom * mass 3.1575
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group all type 1 4
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# oxDNA bond interactions - FENE backbone
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bond_style oxdna_fene
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bond_style oxdna/fene
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bond_coeff * 2.0 0.25 0.7525
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# oxDNA pair interactions
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pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk
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pair_coeff * * oxdna_excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna_stk 1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna_hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna_hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna_hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna_xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk 1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,96 @@
|
|||
# LAMMPS data file
|
||||
16 atoms
|
||||
16 ellipsoids
|
||||
13 bonds
|
||||
|
||||
4 atom types
|
||||
1 bond types
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 3.1575
|
||||
2 3.1575
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 2 5.999771538385027e-01 -5.235921299024461e-03 1.948814275651561e+00 1 1 1
|
||||
7 3 4.890766774371325e-01 3.475687034056071e-01 2.338577130781873e+00 1 1 1
|
||||
8 4 1.923677943514057e-01 5.683261666476170e-01 2.728339985912185e+00 1 1 1
|
||||
9 1 -1.923677943514057e-01 -5.683261666476170e-01 2.728339985912185e+00 2 1 1
|
||||
10 2 -4.890766774371324e-01 -3.475687034056071e-01 2.338577130781873e+00 2 1 1
|
||||
11 3 -5.999771538385025e-01 5.235921299024461e-03 1.948814275651561e+00 2 1 1
|
||||
12 4 -4.829362784135481e-01 3.560513319622207e-01 1.559051420521249e+00 2 1 1
|
||||
13 1 -1.824198365552940e-01 5.715968887521514e-01 1.169288565390936e+00 2 1 1
|
||||
14 2 1.874009511073395e-01 5.699832309147912e-01 7.795257102606241e-01 2 1 1
|
||||
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
|
||||
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 4.363309284746654e-03 0.000000000000000e+00 0.000000000000000e+00 9.999904807207346e-01
|
||||
7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -3.040330609254902e-01 0.000000000000000e+00 0.000000000000000e+00 9.526614812535865e-01
|
||||
8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.828323126827837e-01 0.000000000000000e+00 0.000000000000000e+00 -8.125924533816677e-01
|
||||
9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.125924533816681e-01 5.828323126827832e-01 -0.000000000000000e+00
|
||||
10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.526614812535864e-01 3.040330609254902e-01 0.000000000000000e+00
|
||||
11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.999904807207346e-01 -4.363309284746654e-03 0.000000000000000e+00
|
||||
12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246526e-01 -3.123349185122325e-01 0.000000000000000e+00
|
||||
13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847402e-01 -5.899012371043603e-01 0.000000000000000e+00
|
||||
14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357898e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252948e-01 0.000000000000000e+00
|
||||
16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 2.775557561562893e-17 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
|
|
@ -24,18 +24,18 @@ set atom * mass 3.1575
|
|||
group all type 1 4
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna_fene
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk
|
||||
pair_coeff * * oxdna_excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna_stk 1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna_hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna_hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna_hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna_xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk 1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,59 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Oliver Henrich (EPCC, University of Edinburgh)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdlib.h>
|
||||
#include "bond_oxdna2_fene.h"
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "update.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "atom_vec_ellipsoid.h"
|
||||
#include "math_extra.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondOxdna2Fene::BondOxdna2Fene(LAMMPS *lmp) : BondOxdnaFene(lmp)
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondOxdna2Fene::~BondOxdna2Fene()
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute vector COM-sugar-phosphate backbone interaction site in oxDNA2
|
||||
------------------------------------------------------------------------- */
|
||||
void BondOxdna2Fene::compute_interaction_sites(double e1[3],
|
||||
double e2[3], double r[3])
|
||||
{
|
||||
double d_cs_x=-0.34, d_cs_y=+0.3408;
|
||||
|
||||
r[0] = d_cs_x*e1[0] + d_cs_y*e2[0];
|
||||
r[1] = d_cs_x*e1[1] + d_cs_y*e2[1];
|
||||
r[2] = d_cs_x*e1[2] + d_cs_y*e2[2];
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Oliver Henrich (EPCC, University of Edinburgh)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef BOND_CLASS
|
||||
|
||||
BondStyle(oxdna2/fene,BondOxdna2Fene)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_BOND_OXDNA2_FENE_H
|
||||
#define LMP_BOND_OXDNA2_FENE_H
|
||||
|
||||
#include "bond_oxdna_fene.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class BondOxdna2Fene : public BondOxdnaFene {
|
||||
public:
|
||||
BondOxdna2Fene(class LAMMPS *);
|
||||
virtual ~BondOxdna2Fene();
|
||||
virtual void compute_interaction_sites(double *, double *, double *);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
W: FENE bond too long: %ld %d %d %g
|
||||
|
||||
A FENE bond has stretched dangerously far. It's interaction strength
|
||||
will be truncated to attempt to prevent the bond from blowing up.
|
||||
|
||||
E: Bad FENE bond
|
||||
|
||||
Two atoms in a FENE bond have become so far apart that the bond cannot
|
||||
be computed.
|
||||
|
||||
E: Incorrect args for bond coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
W: Use special bonds = 0,1,1 with bond style oxdna
|
||||
|
||||
Most FENE models need this setting for the special_bonds command.
|
||||
|
||||
W: FENE bond too long: %ld %g
|
||||
|
||||
A FENE bond has stretched dangerously far. It's interaction strength
|
||||
will be truncated to attempt to prevent the bond from blowing up.
|
||||
|
||||
*/
|
||||
|
|
@ -51,6 +51,21 @@ BondOxdnaFene::~BondOxdnaFene()
|
|||
}
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute vector COM-sugar-phosphate backbone interaction site in oxDNA
|
||||
------------------------------------------------------------------------- */
|
||||
void BondOxdnaFene::compute_interaction_sites(double e1[3],
|
||||
double e2[3], double r[3])
|
||||
{
|
||||
double d_cs=-0.4;
|
||||
|
||||
r[0] = d_cs*e1[0];
|
||||
r[1] = d_cs*e1[1];
|
||||
r[2] = d_cs*e1[2];
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute function for oxDNA FENE-bond interaction
|
||||
s=sugar-phosphate backbone site, b=base site, st=stacking site
|
||||
|
|
@ -62,8 +77,6 @@ void BondOxdnaFene::compute(int eflag, int vflag)
|
|||
double delr[3],ebond,fbond;
|
||||
double rsq,Deltasq,rlogarg;
|
||||
double r,rr0,rr0sq;
|
||||
// distances COM-backbone site
|
||||
double d_cs=-0.24;
|
||||
// vectors COM-backbone site in lab frame
|
||||
double ra_cs[3],rb_cs[3];
|
||||
|
||||
|
|
@ -100,12 +113,8 @@ void BondOxdnaFene::compute(int eflag, int vflag)
|
|||
MathExtra::q_to_exyz(qb,bx,by,bz);
|
||||
|
||||
// vector COM-backbone site a and b
|
||||
ra_cs[0] = d_cs*ax[0];
|
||||
ra_cs[1] = d_cs*ax[1];
|
||||
ra_cs[2] = d_cs*ax[2];
|
||||
rb_cs[0] = d_cs*bx[0];
|
||||
rb_cs[1] = d_cs*bx[1];
|
||||
rb_cs[2] = d_cs*bx[2];
|
||||
compute_interaction_sites(ax,ay,ra_cs);
|
||||
compute_interaction_sites(bx,by,rb_cs);
|
||||
|
||||
// vector backbone site b to a
|
||||
delr[0] = x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0];
|
||||
|
|
|
|||
|
|
@ -16,7 +16,7 @@
|
|||
|
||||
#ifdef BOND_CLASS
|
||||
|
||||
BondStyle(oxdna_fene,BondOxdnaFene)
|
||||
BondStyle(oxdna/fene,BondOxdnaFene)
|
||||
|
||||
#else
|
||||
|
||||
|
|
@ -31,6 +31,7 @@ class BondOxdnaFene : public Bond {
|
|||
public:
|
||||
BondOxdnaFene(class LAMMPS *);
|
||||
virtual ~BondOxdnaFene();
|
||||
virtual void compute_interaction_sites(double *, double *, double *);
|
||||
virtual void compute(int, int);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
|
|
|
|||
|
|
@ -31,6 +31,8 @@ namespace MFOxdna {
|
|||
inline double DF4(double, double, double, double, double, double);
|
||||
inline double F5(double, double, double, double, double);
|
||||
inline double DF5(double, double, double, double, double);
|
||||
inline double F6(double, double, double);
|
||||
inline double DF6(double, double, double);
|
||||
inline double is_3pto5p(const double *, const double *);
|
||||
|
||||
}
|
||||
|
|
@ -252,6 +254,32 @@ inline double MFOxdna::DF5(double x, double a, double x_ast,
|
|||
return 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
f6 modulation factor
|
||||
------------------------------------------------------------------------- */
|
||||
inline double MFOxdna::F6(double theta, double a, double b)
|
||||
{
|
||||
if (theta < b) {
|
||||
return 0.0;
|
||||
}
|
||||
else {
|
||||
return 0.5 * a * (theta-b)*(theta-b);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
derivative of f6 modulation factor
|
||||
------------------------------------------------------------------------- */
|
||||
inline double MFOxdna::DF6(double theta, double a, double b)
|
||||
{
|
||||
if (theta < b) {
|
||||
return 0.0;
|
||||
}
|
||||
else {
|
||||
return a * (theta-b);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
test for directionality by projecting base normal n onto delr = a - b,
|
||||
returns 1 if nucleotide b to nucleotide a is 3' to 5', otherwise -1
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,88 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Oliver Henrich (EPCC, University of Edinburgh)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(oxdna2/coaxstk,PairOxdna2Coaxstk)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_OXDNA2_COAXSTK_H
|
||||
#define LMP_PAIR_OXDNA2_COAXSTK_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairOxdna2Coaxstk : public Pair {
|
||||
public:
|
||||
PairOxdna2Coaxstk(class LAMMPS *);
|
||||
virtual ~PairOxdna2Coaxstk();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
void init_list(int, class NeighList *);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
void *extract(const char *, int &);
|
||||
|
||||
protected:
|
||||
// coaxial stacking interaction
|
||||
double **k_cxst, **cut_cxst_0, **cut_cxst_c, **cut_cxst_lo, **cut_cxst_hi;
|
||||
double **cut_cxst_lc, **cut_cxst_hc, **b_cxst_lo, **b_cxst_hi;
|
||||
double **cutsq_cxst_hc;
|
||||
|
||||
double **a_cxst1, **theta_cxst1_0, **dtheta_cxst1_ast;
|
||||
double **b_cxst1, **dtheta_cxst1_c;
|
||||
|
||||
double **a_cxst4, **theta_cxst4_0, **dtheta_cxst4_ast;
|
||||
double **b_cxst4, **dtheta_cxst4_c;
|
||||
|
||||
double **a_cxst5, **theta_cxst5_0, **dtheta_cxst5_ast;
|
||||
double **b_cxst5, **dtheta_cxst5_c;
|
||||
|
||||
double **a_cxst6, **theta_cxst6_0, **dtheta_cxst6_ast;
|
||||
double **b_cxst6, **dtheta_cxst6_c;
|
||||
|
||||
double **AA_cxst1, **BB_cxst1;
|
||||
|
||||
virtual void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,71 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Oliver Henrich (EPCC, University of Edinburgh)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "pair_oxdna2_excv.h"
|
||||
#include "mf_oxdna.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "update.h"
|
||||
#include "integrate.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "atom_vec_ellipsoid.h"
|
||||
#include "math_extra.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
using namespace MFOxdna;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairOxdna2Excv::PairOxdna2Excv(LAMMPS *lmp) : PairOxdnaExcv(lmp)
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairOxdna2Excv::~PairOxdna2Excv()
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute vector COM-excluded volume interaction sites in oxDNA2
|
||||
------------------------------------------------------------------------- */
|
||||
void PairOxdna2Excv::compute_interaction_sites(double e1[3],
|
||||
double e2[3], double rs[3], double rb[3])
|
||||
{
|
||||
double d_cs_x=-0.34, d_cs_y=+0.3408, d_cb=+0.4;
|
||||
|
||||
rs[0] = d_cs_x*e1[0] + d_cs_y*e2[0];
|
||||
rs[1] = d_cs_x*e1[1] + d_cs_y*e2[1];
|
||||
rs[2] = d_cs_x*e1[2] + d_cs_y*e2[2];
|
||||
|
||||
rb[0] = d_cb*e1[0];
|
||||
rb[1] = d_cb*e1[1];
|
||||
rb[2] = d_cb*e1[2];
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Oliver Henrich (EPCC, University of Edinburgh)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(oxdna2/excv,PairOxdna2Excv)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_OXDNA2_EXCV_H
|
||||
#define LMP_PAIR_OXDNA2_EXCV_H
|
||||
|
||||
#include "pair_oxdna_excv.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairOxdna2Excv : public PairOxdnaExcv {
|
||||
public:
|
||||
PairOxdna2Excv(class LAMMPS *);
|
||||
virtual ~PairOxdna2Excv();
|
||||
virtual void compute_interaction_sites(double *,
|
||||
double *, double *, double *);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
*/
|
||||
|
|
@ -127,7 +127,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
|
|||
double dcdrax,dcdray,dcdraz;
|
||||
|
||||
// distances COM-backbone site, COM-stacking site
|
||||
double d_cs=-0.24, d_cst=0.5;
|
||||
double d_cs=-0.4, d_cst=+0.34;
|
||||
// vectors COM-backbone site, COM-stacking site in lab frame
|
||||
double ra_cs[3],ra_cst[3];
|
||||
double rb_cs[3],rb_cst[3];
|
||||
|
|
|
|||
|
|
@ -16,7 +16,7 @@
|
|||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(oxdna_coaxstk,PairOxdnaCoaxstk)
|
||||
PairStyle(oxdna/coaxstk,PairOxdnaCoaxstk)
|
||||
|
||||
#else
|
||||
|
||||
|
|
|
|||
|
|
@ -88,6 +88,24 @@ PairOxdnaExcv::~PairOxdnaExcv()
|
|||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute vector COM-excluded volume interaction sites in oxDNA
|
||||
------------------------------------------------------------------------- */
|
||||
void PairOxdnaExcv::compute_interaction_sites(double e1[3],
|
||||
double e2[3], double rs[3], double rb[3])
|
||||
{
|
||||
double d_cs=-0.4, d_cb=+0.4;
|
||||
|
||||
rs[0] = d_cs*e1[0];
|
||||
rs[1] = d_cs*e1[1];
|
||||
rs[2] = d_cs*e1[2];
|
||||
|
||||
rb[0] = d_cb*e1[0];
|
||||
rb[1] = d_cb*e1[1];
|
||||
rb[2] = d_cb*e1[2];
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute function for oxDNA pair interactions
|
||||
s=sugar-phosphate backbone site, b=base site, st=stacking site
|
||||
|
|
@ -146,18 +164,13 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
|
|||
qa=bonus[a].quat;
|
||||
MathExtra::q_to_exyz(qa,ax,ay,az);
|
||||
|
||||
// position of backbone site a
|
||||
ra_cs[0] = d_cs*ax[0];
|
||||
ra_cs[1] = d_cs*ax[1];
|
||||
ra_cs[2] = d_cs*ax[2];
|
||||
// vector COM - backbone and base site a
|
||||
compute_interaction_sites(ax,ay,ra_cs,ra_cb);
|
||||
|
||||
rtmp_s[0] = x[a][0] + ra_cs[0];
|
||||
rtmp_s[1] = x[a][1] + ra_cs[1];
|
||||
rtmp_s[2] = x[a][2] + ra_cs[2];
|
||||
|
||||
// position of base site a
|
||||
ra_cb[0] = d_cb*ax[0];
|
||||
ra_cb[1] = d_cb*ax[1];
|
||||
ra_cb[2] = d_cb*ax[2];
|
||||
rtmp_b[0] = x[a][0] + ra_cb[0];
|
||||
rtmp_b[1] = x[a][1] + ra_cb[1];
|
||||
rtmp_b[2] = x[a][2] + ra_cb[2];
|
||||
|
|
@ -176,12 +189,8 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
|
|||
qb=bonus[b].quat;
|
||||
MathExtra::q_to_exyz(qb,bx,by,bz);
|
||||
|
||||
rb_cs[0] = d_cs*bx[0];
|
||||
rb_cs[1] = d_cs*bx[1];
|
||||
rb_cs[2] = d_cs*bx[2];
|
||||
rb_cb[0] = d_cb*bx[0];
|
||||
rb_cb[1] = d_cb*bx[1];
|
||||
rb_cb[2] = d_cb*bx[2];
|
||||
// vector COM - backbone and base site b
|
||||
compute_interaction_sites(bx,by,rb_cs,rb_cb);
|
||||
|
||||
// vector backbone site b to a
|
||||
delr_ss[0] = rtmp_s[0] - (x[b][0] + rb_cs[0]);
|
||||
|
|
|
|||
|
|
@ -16,7 +16,7 @@
|
|||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(oxdna_excv,PairOxdnaExcv)
|
||||
PairStyle(oxdna/excv,PairOxdnaExcv)
|
||||
|
||||
#else
|
||||
|
||||
|
|
@ -31,6 +31,8 @@ class PairOxdnaExcv : public Pair {
|
|||
public:
|
||||
PairOxdnaExcv(class LAMMPS *);
|
||||
virtual ~PairOxdnaExcv();
|
||||
virtual void compute_interaction_sites(double *, double *,
|
||||
double *, double *);
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
|
|
|
|||
|
|
@ -125,7 +125,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
|
|||
double theta8,t8dir[3],cost8;
|
||||
|
||||
// distance COM-hbonding site
|
||||
double d_chb=0.56;
|
||||
double d_chb=+0.4;
|
||||
// vectors COM-h-bonding site in lab frame
|
||||
double ra_chb[3],rb_chb[3];
|
||||
|
||||
|
|
|
|||
|
|
@ -16,7 +16,8 @@
|
|||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(oxdna_hbond,PairOxdnaHbond)
|
||||
PairStyle(oxdna/hbond,PairOxdnaHbond)
|
||||
PairStyle(oxdna2/hbond,PairOxdnaHbond)
|
||||
|
||||
#else
|
||||
|
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@ -116,7 +116,7 @@ void PairOxdnaStk::compute(int eflag, int vflag)
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double cosphi1,cosphi2,cosphi1dir[3],cosphi2dir[3];
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// distances COM-backbone site, COM-stacking site
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double d_cs=-0.24, d_cst=0.5;
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double d_cs=-0.4, d_cst=+0.34;
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// vectors COM-backbone site, COM-stacking site in lab frame
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double ra_cs[3],ra_cst[3];
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double rb_cs[3],rb_cst[3];
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@ -16,7 +16,8 @@
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#ifdef PAIR_CLASS
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PairStyle(oxdna_stk,PairOxdnaStk)
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PairStyle(oxdna/stk,PairOxdnaStk)
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PairStyle(oxdna2/stk,PairOxdnaStk)
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#else
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@ -125,7 +125,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
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double theta8,theta8p,t8dir[3],cost8;
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// distance COM-h-bonding site
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double d_chb=0.56;
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double d_chb=+0.4;
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// vectors COM-h-bonding site in lab frame
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double ra_chb[3],rb_chb[3];
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@ -16,7 +16,8 @@
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#ifdef PAIR_CLASS
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PairStyle(oxdna_xstk,PairOxdnaXstk)
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PairStyle(oxdna/xstk,PairOxdnaXstk)
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PairStyle(oxdna2/xstk,PairOxdnaXstk)
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||||
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||||
#else
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue