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Included values in real units

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This commit is contained in:
Oliver Henrich
2024-05-22 16:00:58 +01:00
parent 938d117890
commit ad81558fe0
3 changed files with 14 additions and 14 deletions
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8
doc/src/pair_oxdna.rst
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@ -37,12 +37,12 @@ Syntax
*oxdna/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
T = temperature (oxDNA units, 0.1 = 300 K)
xi = 1.3448 (temperature-independent coefficient in stacking strength)
kappa = 2.6568 (coefficient of linear temperature dependence in stacking strength)
T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K)
xi = 1.3448 (LJ units) or 8.01727944817084 (real units), temperature-independent coefficient in stacking strength
kappa = 2.6568 (LJ units) or 0.005279604 (real units), coefficient of linear temperature dependence in stacking strength
*oxdna/hbond* args = seq eps 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
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs)
eps = 1.077 (LJ units) or 6.42073911784652 (real units), average hydrogen bonding strength between A-T and C-G Watson-Crick base pairs, 0 between all other pairs
Examples
""""""""

10
doc/src/pair_oxdna2.rst
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@ -41,14 +41,14 @@ Syntax
*oxdna2/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
T = temperature (oxDNA units, 0.1 = 300 K)
xi = 1.3523 (temperature-independent coefficient in stacking strength)
kappa = 2.6717 (coefficient of linear temperature dependence in stacking strength)
T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K)
xi = 1.3523 (LJ units) or 8.06199211612242 (real units), temperature-independent coefficient in stacking strength
kappa = 2.6717 (LJ units) or 0.005309213 (real units), coefficient of linear temperature dependence in stacking strength
*oxdna2/hbond* args = seq eps 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
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
eps = 1.0678 (LJ units) or 6.36589157849259 (real units), average hydrogen bonding strength between A-T and C-G Watson-Crick base pairs, 0 between all other pairs
*oxdna2/dh* args = T rhos qeff
T = temperature (oxDNA units, 0.1 = 300 K)
T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K)
rhos = salt concentration (mole per litre)
qeff = 0.815 (effective charge in elementary charges)

10
doc/src/pair_oxrna2.rst
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@ -41,14 +41,14 @@ Syntax
*oxrna2/stk* args = seq T xi kappa 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
T = temperature (oxDNA units, 0.1 = 300 K)
xi = 1.40206 (temperature-independent coefficient in stacking strength)
kappa = 2.77 (coefficient of linear temperature dependence in stacking strength)
T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K)
xi = 1.40206 (LJ units) or 8.35864576375849 (real units), temperature-independent coefficient in stacking strength
kappa = 2.77 (LJ units) or 0.005504556 (real units), coefficient of linear temperature dependence in stacking strength
*oxrna2/hbond* args = seq eps 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
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
eps = 0.870439 (between base pairs A-T, C-G and G-T) or 0 (all other pairs)
eps = 0.870439 (LJ units) or 5.18928666388042 (real units), average hydrogen bonding strength between A-U and C-G Watson-Crick and G-U wobble base pairs, 0 between all other pairs
*oxrna2/dh* args = T rhos qeff
T = temperature (oxDNA units, 0.1 = 300 K)
T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K)
rhos = salt concentration (mole per litre)
qeff = 1.02455 (effective charge in elementary charges)