Errata

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Scientific publications Philippe Hünenberger: typos and minor errors

This page provides a list of typos and minor errors discovered in my publications after printing (please, don't hesitate to contact me if you find others); two articles, [17] and [55], were affected by more significant errors, justifying the publication of an erratum.

The numbering refers to my publication list

[14] Hünenberger & McCammon, J. Chem. Phys. 110 1856 (1999)

  • Page 1868, Eq(A11): δj,I should be replaced by δj,J and δk,I by δk,K
  • Page 1868, Eq(A11) is incorrect as written: the 6 terms in lines 2-4 of Eq(A6) should be added to the left-hand-side of this equation

[17] Baker et al., J. Chem. Phys. 110 10679 (1999)

  • Page 10688, Eq(66): the sign of the last term in the right-hand side should be minus instead of plus, see our book p 79 [Eq(3.42) and following lines] where this error was reported
  • See also Erratum: J. Chem. Phys. 113 2510 (2000)

[18] Hünenberger, In "Simulation and theory of electrostatic interactions in solution..." pp 17-83 (1999)

  • Page 27, Figure 4: The labels of the LΨ and LΨη curves should be swapped, i.e. LΨη is the solid line and LΨ the short-dashed line
  • Page 34, 9 lines below header "Shaping functions": -2.837927 should be replaced by -2.837297

[22] Heinz et al., J. Chem. Phys. 115 1125 (2001)

  • Page 1127, 4 lines below Eq(14): p~α(nΔN) should read p~α(nΔM)

[25] Börjesson & Hünenberger, J. Chem. Phys. 114 9706 (2001)

  • Page 9708, Eq(6): in the right-hand side of the equation, the sum over the 2N vectors l (all possible N-dimensional vectors with components equal to 0 or 1) should actually involve terms that are products from i=1 to N of the indicated quantity
  • Page 9708, Eq(6): this equation is also somewhat clumsy, because it implies the convention 00=1 (this case can occur when λi=0 or λi=1)
  • Page 9708, Eq(6): finally, the Hamiltonian H in the right-hand side should probably rather be called Hphy, and corresponds to physical (0 or 1) protonation states (otherwise, it seems that Htot is used in this equation to define itself)
  • This article has been criticised by Baptista, J. Chem. Phys. 116 7766 (2002); we think at present that the criticism is justified, and agree that the proposed constant-pH method is empirical in nature (mean-field approximation), rather than formally rigorous, as initially thought

[37] Pereira et al., Biophys. J. 86 2273 (2004)

  • Table 1, 3 entries at 475K: the reported values for Dxy and Dz should be divided by 10, see [56] p 15575 (Table 1, footnote a) where this error was reported
  • Figure 4, graph legend: CH2 Glycerol should read CH1 Glycerol

[41] Hünenberger, Adv. Polymer. Sci. 173 105 (2005)

  • Table 1, entry μPR: the name of the ensemble should be "grand-isoenthalpic-isobaric" and not "grand-isothermal-isobaric"
  • Page 114, Eq(12): the quantity summed over i in the right-hand side should read mi[(ri-rCM)21 - (ri-rCM) ⊗(ri-rCM)] instead of mi(ri-rCM) ⊗(ri-rCM)
  • Page 128, Eq(56): the prefactor in the right-hand-side should be -1/2 instead of 1/2
  • Page 128, Eq(57): the prefactor of the second term in the right-hand-side should be +1/2 instead of -1/2
  • Page 143, Eq(113), line 3: left-hand-side, in -∂ρ/∂γ⋅γ, the second γ should be γ-dot (dot overscript)

[47] Heinz & Hünenberger, J. Chem. Phys. 123 034107 (2005)

  • Page 4, Eq(9): the second sum should involve index j instead of i
  • Page 5, 6 lines below Eq(25): -2.837927 should be replaced by -2.837297
  • Page 7, Eq(41): the second sum should involve index j instead of i
  • Page 9, Eq(65): the quantity k3RRF in the denominator of one of the fractions (second line) should actually be k3R3RF
  • Page 9, Eq(65): the last condition k≠0 (bottom of the second line) should actually be k=0
  • Page 18, Eq(C1): e2/4 should be replaced by e2/4

[49] Christen et al., J. Comput. Chem. 26 1719 (2005)

  • Table 7, entry p=3: wp(ξ) should read 3/4-ξ2 instead of -(3/4)(4ξ2-1)

[50] Kastenholz & Hünenberger, J. Chem. Phys. 124 124106 (2006)

  • Page 8, Point (1): the estimated value of ΔΦODL for liquid argon at 87K based on the Slater-type analysis should be -411 kJ mol-1e-1 (-4.26 V) instead of -463 kJ mol-1e-1 (-4.80 V), see below
  • Supplementary Material, Eq(S2.2): η should be 21.6 instead of 24.3 nm-3, and ΔΦQMODLshould be -411 instead of -463 kJ mol-1e-1, the reason is that the molar mass of argon was erroneously set to 35.45 instead of 39.948 g mol-1, see our book p 283 [Eq(4.342) and following lines], 284 [Eq(4.347) and following lines] and 285, where the correct results are reported

[51] Kastenholz & Hünenberger, J. Chem. Phys. 124 224501 (2006)

  • Table III, entries LS/2048, LA/2048 and LV/2048: box edge (3rd column) should be 3.94 instead of 3.13 nm
  • Page 7, 4 lines below Eq(39): one could expect the correction term to be proportional to (1-εS-1), and not (1-εS)-1 as written; however, even in this altered form, the statement is not correct, see [85] p 5 [comment just below Eq(15)] or our book p 504 (comment just below Table 6.2), where the statement is ammended

[55] Pereira et al., Biophys. J. 90 4337 (2006)

  • Figure 1, drawing for Nigerose (N): the arrow marked 49.5% should point in the opposite direction, see Table 1 where the H-bond considered is (correctly) reported in the direction HO4'→O2
  • Table 1, caption, lines 1-2: the ω' values should read gg -60° and gt +60°, see [79] pp 1784-1786 and 1790 as well as [84] pp 1002-1004 for precise (and correct) definitions
  • See also Erratum: Biophys. J. 93 706 (2007)
  • The erratum also contains a serious mistake in its Table 1: the entries ΔSclah and ΔSclpc should be multiplied by 8.314, and the entries Sctd and -TΔSctd recalculated accordingly, see [79] p 1796 where this error was reported

[57] Baron et al., Trends Phys. Chem. 11 87 (2006)

  • Page 118, Eq(C5): the left-hand-side of this equation should read ln κ1o instead of κ1o
  • Page 118, Eq(C6): the left-hand-side of this equation should read ln κ2o instead of κ2o

[66] Perić et al., 34 421 (2008)

  • Abstract, line 3: abreviation for poly-α(1→4)-L-guluronate should read pGulU instead of pGlcU

[65] Kräutler & Hünenberger, Mol. Simul. 34 491 (2008)

  • Figure 4: the radial distribution functions are incorrectly normalized, probably to unity (three bottom panels) or half-unity (top panel) instead of the box volume Vbox (i.e. the integral of 4πr2g(r) is one or one-half instead of Vbox); the reported g(r) have thus units of nm-3 and must be scaled by Vbox (three bottom panels) or 2Vbox (top panel) with Vbox = 287.5 (CU box) or 228.3 (TO box) nm3 to obtain properly normalized (unitless) radial distribution functions.

[81] Horta et al., J. Chem. Theory Comput. 6 2488 (2010)

  • Page 2491, 15 lines below Table 1: a value of 4.575·10-4 (kJ·mol-1·nm-3)-1 was used for the simulations, but it is not the value appropriate for pure water, which would be 7.505·10-4 (kJ·mol-1·nm-3)-1 based on a compressibility of 4.52·10-5 bar-1 at 25°C; the value used is the approximate value suggested in the GROMOS96 manual for a 1:1 protein-water mixture
  • Page 2493, Table 3: the numbers reported in this table and discussed in the text for NLLintra and NWW are actually not the average numbers of intralayer lipid-lipid and water-water H-bonds, respectively, but twice these numbers; given this doubling, the scaling of NLLintra by the number of lipids in the system provides the average number of lipids H-bonded to a given lipid within a leaflet, and the discussion on page 2493 (right column, second paragraph) is correct; note that unlike NLLintra, NLLinter is not doubled, i.e. it is the average number of interlayer lipid-lipid H-bonds; this is a nomenclature issue and not a mistake, see [99] for a more consistent formulation
  • Page 2493, Table 3: in addition to the previous nomenclature issue, the numbers reported in this table for NLLintra (i.e. twice the average number of intralayer lipid-lipid H-bonds) are affected by a small calculation mistake; the correct values can be obtained by subtracting NLLinter from these numbers; the error is essentially negligible (with the possible exception of the three last entries at quarter hydration) and does not affect the main conclusions of the discussion on page 2493 (right column, second paragraph)
  • Page 2497, Figure 5, points at n=2: the values for these points are affected by a small calculation error and are too low (this problem also affects [99], Figure 3), see [104] (caption of Figure 9) and [105] (caption of Figure 8) where the error was reported and correct values for these points can be found

[82] Hansen et al., J. Chem. Theory Comput. 6 2596 (2010)

  • Page 2617, 6 lines below Eq (A.8): kLE is equal to (2πσ)NLE/2cLE and not (2πσ)NLE/2cLE

[83] Hansen & Hünenberger, J. Chem. Theory Comput. 6 2622 (2010)

  • Page 2627, 4 lines above Eq (5): Wl should be referred to as a "half" width instead of a "double" width, i.e. the width of the "tube" defined by the flat-bottom region of the transverse biasing potential is 2Wl
  • Page 2631, Eq(27): this equation as well as the following descriptive lines are formally incorrect (although the calculations were performed correctly); <X(r)>Q(r)∈S should be replaced by <X(r)θ(r)> where θ(r) is one if Q(r)∈S and zero otherwise, and the averaging is performed over the entire biased ensemble; since CG can be chosen arbitrarily, this is equivalent to an integral (and not an average) over the region for which Q(r)∈S

[84] Hansen & Hünenberger, J. Comput. Chem. 32 998 (2011)

  • Table 2, last line, improper dihedrals for β-Glc: C2-C1-O1-C2 must be changed to C2-C3-C1-O2, and C5-O5-C6-C4 to C5-C4-O5-C6
  • Table 3, entry C6: 45A4/53A6 as well as 56ACARBO atom types are incorrect and should both be CH2
  • Tables 3 and 4: the atom type HO actually does not exist in GROMOS - in the force-field files, it is listed simply as H
  • Table 6, entry T1, dihedrals for β-Glc: O5-C5-C6-O6 should rather be defined as C4-C5-C6-O6 to follow the the IUPAC definition of ω; this does not matter much in practice since T1 is a 3-fold term (the definition C4-C5-C6-O6 is adopted in the current GROMOS force-field files)
  • Table 6, entry T3, dihedrals for β-Glc: C5-C4-O4-H4 should rather be defined as C3-C4-O4-H4 to follow the systematism of the other dihedrals and the IUPAC definition of χ4; this does not matter much in practice since T3 is a 3-fold term (the definition C3-C4-O4-H4 is adopted in the current GROMOS force-field files)
  • Table 8, Gal ω-rotamers, entry for 45A4(β) from Ref 73: the populations should be 34, 41 and 25 (instead of 34, 41 and 35)

[85] Reif & Hünenberger, J. Chem. Phys. 134 144103 (2011)

  • Page 7, Eq. 32: This equation is formally not correct, considering that qI=0 in the situation considered here. One should write instead: χion = Φoraw + [2/(NA qI) ΔGBLS]* + [1/(NA qI) ΔGC1LS]*, where the "*" superscript indicates that the quantity is simplified assuming qI≠0 and subsequently evaluated at qI=0. From Eq. 18, the second term in the right-hand-side is zero. From Eq. 24, the third term in the right-hand-side is -NA[1-4πRI3/(3 L3)]ξ'S
  • Page 7, Eq. 33: In contrast to the preceding one, this equation considers qI to be the full ionic charge. Following from the previous comment, the second term in the parenthesis of the right-hand-side should be zero, i.e. the equation is incorrect and should read ΔGC1LS = 4πRI3/(3 L3) (NAqIΦoraw+ΔGC1LS). Note that the error affects the article but not the calculation results, which actually relied on the correct equation

[86] Reif & Hünenberger, J. Chem. Phys. 134 144104 (2011)

  • Figure 2: a strange "20p0" artifact (in black) has appeared in the middle of the figure upon printing (should be ignored)

[88] Horta et al., J. Chem. Theory Comput. 7 10161 (2011)

  • Table 4, entry ether/OE: charge in 53A6variant should be -0.420 instead of 0.420
  • Table 4, entry aldehyde/O: charge in 53A6OXY should be -0.475 instead of 0.475
  • Table 7, entry 53A6OXY for DXE: hydration free energy ΔGwat should be -16.1 +/- 1.8 kJ/mol instead of -18.5 kJ/mol +/- 1.8 (the reported value was mistakenly calculated using a slightly modified OCCO torsional-energy term), see [98] Table 6 where this error was reported (this value is also recalculated therein using a slightly different calculation protocol but the normal OCCO torsional-energy term of 53A6OXY, resulting in -14.7 +/- 0.1 kJ/mol)
  • Page 1023, left column, line 23: a value of 4.575·10-4 (kJ·mol-1·nm-3)-1 was used for the simulations in water, but it is not the value appropriate for pure water, which would be 7.505·10-4 (kJ·mol-1·nm-3)-1, see corresponding note under [81]; the error incurred is probably negligible, considering that this parameter is combined with the arbitrary barostat coupling time, which has itself a very limited influence on the thermodynamic properties of the system

[90] Choutko et al., Chem. Phys. Chem. 12 3214 (2012)

  • Page 3219, left column, lines 29-30: "a slight excess of W2L over WL water units is observed at the wall" should be "a slight excess of WL over W2L water units is observed at the wall"

[93] Kunz et al., J. Comput. Chem. 33 340 (2012)

  • Page 342, Eq. 18: the first summation over index i should be deleted, and the second summation replaced by a summation over j≠i instead of j>i.

[98] Fuchs et al., J. Chem. Theory Comput. 8 3943 (2012)

  • Table 7, entry rms for 53A6OXYrec: "[0.03]" should read "[0.04]" (rounding error).
  • Table 7, entry rms for 53A6OXY+D: "[0.97]" should read "[0.03]".

[99] Laner et al., Mol. Simul. 39 563 (2013)

  • Page 579, left column, line 11: in terms of entropy, the factor is about 2.7 (122.2/46) and not 3.8, see [Laner,KIN] p XXX where this error was reported (a value of 2.5 is actually proposed therein based on more extensive simulations)
  • Page 576, Figure 4, points at n=11: the values for these points are affected by a small calculation error and are too low (this problem also affects [81], Figure 5), see [104] (caption of Figure 9) and [105] (caption of Figure 8) where the error was reported and correct values for these points can be found

[101] Wang et al., Eur. Biophys. J. 42 521 (2013)

  • Page 534, left column, line 40: "it contributes to affinity and not to specificity, and is thus a steering force" should read "it contributes to specificity and not to affinity, and is thus a steering force"

[102] Rocklin et al., J. Chem. Phys. 139 184103 (2013)

  • Page 17, caption Table II, and p 23, caption Table IV : the value of γS should read 0.00764 e nm2 (2*0.417*0.095722 for TIP3P water; instead of 0.0764 as written); this is just a typo, all calculations were performed with the correct value.

[BOOK]

 
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