char *search,*replace;
} t_sandr;
+/* The order of these arrays is significant. Text search and replace
+ * for each element occurs in order, so earlier changes can induce
+ * subsequent changes even though the original text might not appear
+ * to invoke the latter changes. */
+
const t_sandr_const sandrTeX[] = {
{ "[TT]", "{\\tt " },
{ "[tt]", "}" },
{ "&", "\\&" },
/* The next couple of lines allow true Greek symbols to be written to the
manual, which makes it look pretty */
- { "[GRK]", "$\\" },
- { "[grk]", "$" },
+ { "[GRK]", "\\ensuremath{\\" },
+ { "[grk]", "}" },
+ { "[MATH]","\\ensuremath{" },
+ { "[math]","}" },
+ { "[INT]","\\ensuremath{\\int" },
+ { "[FROM]","_" },
+ { "[from]","" },
+ { "[TO]", "^" },
+ { "[to]", "" },
+ { "[int]","}" },
+ { "[SUM]","\\ensuremath{\\sum" },
+ { "[sum]","}" },
+ { "[SUB]","\\ensuremath{_{" },
+ { "[sub]","}}" },
+ { "[SQRT]","\\ensuremath{\\sqrt{" },
+ { "[sqrt]","}}" },
+ { "[EXP]","\\ensuremath{\\exp{(" },
+ { "[exp]",")}}" },
+ { "[LN]","\\ensuremath{\\ln{(" },
+ { "[ln]",")}}" },
+ { "[LOG]","\\ensuremath{\\log{(" },
+ { "[log]",")}}" },
+ { "[COS]","\\ensuremath{\\cos{(" },
+ { "[cos]",")}}" },
+ { "[SIN]","\\ensuremath{\\sin{(" },
+ { "[sin]",")}}" },
+ { "[TAN]","\\ensuremath{\\tan{(" },
+ { "[tan]",")}}" },
+ { "[COSH]","\\ensuremath{\\cosh{(" },
+ { "[cosh]",")}}" },
+ { "[SINH]","\\ensuremath{\\sinh{(" },
+ { "[sinh]",")}}" },
+ { "[TANH]","\\ensuremath{\\tanh{(" },
+ { "[tanh]",")}}" },
/* The next two lines used to substitute "|" and "||" to "or", but only
* g_angle used that functionality, so that was changed to a textual
* "or" there, so that other places could use those symbols to indicate
{ "[bb]", "" },
{ "[IT]", "" },
{ "[it]", "" },
+ { "[MATH]","" },
+ { "[math]","" },
+ { "[INT]","integral" },
+ { "[FROM]"," from " },
+ { "[from]","" },
+ { "[TO]", " to " },
+ { "[to]", " of" },
+ { "[int]","" },
+ { "[SUM]","sum" },
+ { "[sum]","" },
+ { "[SUB]","_" },
+ { "[sub]","" },
+ { "[SQRT]","sqrt(" },
+ { "[sqrt]",")" },
+ { "[EXP]","exp(" },
+ { "[exp]",")" },
+ { "[LN]","ln(" },
+ { "[ln]",")" },
+ { "[LOG]","log(" },
+ { "[log]",")" },
+ { "[COS]","cos(" },
+ { "[cos]",")" },
+ { "[SIN]","sin(" },
+ { "[sin]",")" },
+ { "[TAN]","tan(" },
+ { "[tan]",")" },
+ { "[COSH]","cosh(" },
+ { "[cosh]",")" },
+ { "[SINH]","sinh(" },
+ { "[sinh]",")" },
+ { "[TANH]","tanh(" },
+ { "[tanh]",")" },
{ "[PAR]","\n\n" },
{ "[BR]", "\n"},
{ "[GRK]", "" },
{ "[bb]", "'''" },
{ "[IT]", "''" },
{ "[it]", "''" },
+ { "[MATH]","" },
+ { "[math]","" },
+ { "[INT]","integral" },
+ { "[FROM]"," from " },
+ { "[from]","" },
+ { "[TO]", " to " },
+ { "[to]", " of" },
+ { "[int]","" },
+ { "[SUM]","sum" },
+ { "[sum]","" },
+ { "[SUB]","_" },
+ { "[sub]","" },
+ { "[SQRT]","sqrt(" },
+ { "[sqrt]",")", },
+ { "[EXP]","exp(" },
+ { "[exp]",")" },
+ { "[LN]","ln(" },
+ { "[ln]",")" },
+ { "[LOG]","log(" },
+ { "[log]",")" },
+ { "[COS]","cos(" },
+ { "[cos]",")" },
+ { "[SIN]","sin(" },
+ { "[sin]",")" },
+ { "[TAN]","tan(" },
+ { "[tan]",")" },
+ { "[COSH]","cosh(" },
+ { "[cosh]",")" },
+ { "[SINH]","sinh(" },
+ { "[sinh]",")" },
+ { "[TANH]","tanh(" },
+ { "[tanh]",")" },
{ "[PAR]","\n\n" },
{ "[BR]", "\n" },
{ "[GRK]", "&" },
{ "[bb]", "\\fR" },
{ "[IT]", "\\fI " },
{ "[it]", "\\fR" },
+ { "[MATH]","" },
+ { "[math]","" },
+ { "[INT]","integral" },
+ { "[FROM]"," from " },
+ { "[from]","" },
+ { "[TO]", " to " },
+ { "[to]", " of" },
+ { "[int]","" },
+ { "[SUM]","sum" },
+ { "[sum]","" },
+ { "[SUB]","_" },
+ { "[sub]","" },
+ { "[SQRT]","sqrt(" },
+ { "[sqrt]",")", },
+ { "[EXP]","exp(" },
+ { "[exp]",")" },
+ { "[LN]","ln(" },
+ { "[ln]",")" },
+ { "[LOG]","log(" },
+ { "[log]",")" },
+ { "[COS]","cos(" },
+ { "[cos]",")" },
+ { "[SIN]","sin(" },
+ { "[sin]",")" },
+ { "[TAN]","tan(" },
+ { "[tan]",")" },
+ { "[COSH]","cosh(" },
+ { "[cosh]",")" },
+ { "[SINH]","sinh(" },
+ { "[sinh]",")" },
+ { "[TANH]","tanh(" },
+ { "[tanh]",")" },
{ "[PAR]","\n\n" },
{ "\n ", "\n" },
{ "<", "" },
{ "[bb]", "</b>" },
{ "[IT]", "<it>" },
{ "[it]", "</it>" },
+ { "[MATH]","" },
+ { "[math]","" },
+ { "[INT]","integral" },
+ { "[FROM]"," from " },
+ { "[from]","" },
+ { "[TO]", " to " },
+ { "[to]", " of" },
+ { "[int]","" },
+ { "[SUM]","sum" },
+ { "[sum]","" },
+ { "[SUB]","_" },
+ { "[sub]","" },
+ { "[SQRT]","sqrt(" },
+ { "[sqrt]",")", },
+ { "[EXP]","exp(" },
+ { "[exp]",")" },
+ { "[LN]","ln(" },
+ { "[ln]",")" },
+ { "[LOG]","log(" },
+ { "[log]",")" },
+ { "[COS]","cos(" },
+ { "[cos]",")" },
+ { "[SIN]","sin(" },
+ { "[sin]",")" },
+ { "[TAN]","tan(" },
+ { "[tan]",")" },
+ { "[COSH]","cosh(" },
+ { "[cosh]",")" },
+ { "[SINH]","sinh(" },
+ { "[sinh]",")" },
+ { "[TANH]","tanh(" },
+ { "[tanh]",")" },
{ "[PAR]","<p>" },
{ "[BR]", "<br>" },
{ "[GRK]", "&" },
{ "[bb]", "</emp>" },
{ "[IT]", "<it>" },
{ "[it]", "</it>" },
+ { "[MATH]","" },
+ { "[math]","" },
+ { "[INT]","integral" },
+ { "[FROM]"," from " },
+ { "[from]","" },
+ { "[TO]", " to " },
+ { "[to]", " of" },
+ { "[int]","" },
+ { "[SUM]","sum" },
+ { "[sum]","" },
+ { "[SUB]","_" },
+ { "[sub]","" },
+ { "[SQRT]","sqrt(" },
+ { "[sqrt]",")", },
+ { "[EXP]","exp(" },
+ { "[exp]",")" },
+ { "[LN]","ln(" },
+ { "[ln]",")" },
+ { "[LOG]","log(" },
+ { "[log]",")" },
+ { "[COS]","cos(" },
+ { "[cos]",")" },
+ { "[SIN]","sin(" },
+ { "[sin]",")" },
+ { "[TAN]","tan(" },
+ { "[tan]",")" },
+ { "[COSH]","cosh(" },
+ { "[cosh]",")" },
+ { "[SINH]","sinh(" },
+ { "[sinh]",")" },
+ { "[TANH]","tanh(" },
+ { "[tanh]",")" },
{ "[PAR]","</par>\n<par>" },
{ "[BR]", "<br />" },
{ "[GRK]", "" },
{ "-multi", FALSE, etINT,{&nmultisim},
"Do multiple simulations in parallel" },
{ "-replex", FALSE, etINT, {&repl_ex_nst},
- "Attempt replica exchange every # steps" },
+ "Attempt replica exchange periodically with this period" },
{ "-reseed", FALSE, etINT, {&repl_ex_seed},
"Seed for replica exchange, -1 is generate a seed" },
{ "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
{ "-fitfn", FALSE, etENUM, {s_ffn},
"Fit function" },
{ "-ncskip", FALSE, etINT, {&acf.nskip},
- "Skip N points in the output file of correlation functions" },
+ "Skip this many points in the output file of correlation functions" },
{ "-beginfit", FALSE, etREAL, {&acf.tbeginfit},
"Time where to begin the exponential fit of the correlation function" },
{ "-endfit", FALSE, etREAL, {&acf.tendfit},
static real Abh=1e5,Bbh=32,Cbh=1e-3;
static int npow=12;
t_pargs pa[] = {
- { "-c6", FALSE, etREAL, {&c6}, "c6" },
- { "-cn", FALSE, etREAL, {&cn}, "constant for repulsion" },
- { "-pow", FALSE, etINT, {&npow},"power of the repulsion term" },
- { "-sig", FALSE, etREAL, {&sig}, "sig" },
- { "-eps", FALSE, etREAL, {&eps}, "eps" },
+ { "-c6", FALSE, etREAL, {&c6}, "C6" },
+ { "-cn", FALSE, etREAL, {&cn}, "Constant for repulsion" },
+ { "-pow", FALSE, etINT, {&npow},"Power of the repulsion term" },
+ { "-sig", FALSE, etREAL, {&sig}, "[GRK]sigma[grk]" },
+ { "-eps", FALSE, etREAL, {&eps}, "[GRK]epsilon[grk]" },
{ "-A", FALSE, etREAL, {&Abh}, "Buckingham A" },
{ "-B", FALSE, etREAL, {&Bbh}, "Buckingham B" },
{ "-C", FALSE, etREAL, {&Cbh}, "Buckingham C" },
{ "-qi", FALSE, etREAL, {&qi}, "qi" },
{ "-qj", FALSE, etREAL, {&qj}, "qj" },
- { "-sigfac", FALSE, etREAL, {&sigfac}, "Factor in front of sigma for starting the plot" }
+ { "-sigfac", FALSE, etREAL, {&sigfac}, "Factor in front of [GRK]sigma[grk] for starting the plot" }
};
t_filenm fnm[] = {
{ efXVG, "-o", "potje", ffWRITE }
"Option [TT]-cc[tt] plots the resemblance of set i with a cosine of",
"i/2 periods. The formula is:[BR]"
- "2 (int0-T y(t) cos(i [GRK]pi[grk] t) dt)^2 / int0-T y(t) y(t) dt[BR]",
+ "[MATH]2 ([INT][FROM]0[from][TO]T[to][int] y(t) [COS]i [GRK]pi[grk] t[cos] dt)^2 / [INT][FROM]0[from][TO]T[to][int] y^2(t) dt[math][BR]",
"This is useful for principal components obtained from covariance",
"analysis, since the principal components of random diffusion are",
"pure cosines.[PAR]",
"Option [TT]-ee[tt] produces error estimates using block averaging.",
"A set is divided in a number of blocks and averages are calculated for",
"each block. The error for the total average is calculated from",
- "the variance between averages of the m blocks B_i as follows:",
- "error^2 = Sum (B_i - <B>)^2 / (m*(m-1)).",
+ "the variance between averages of the m blocks B[SUB]i[sub] as follows:",
+ "error^2 = [SUM][sum] (B[SUB]i[sub] - <B>)^2 / (m*(m-1)).",
"These errors are plotted as a function of the block size.",
"Also an analytical block average curve is plotted, assuming",
"that the autocorrelation is a sum of two exponentials.",
"The analytical curve for the block average is:[BR]",
- "f(t) = [GRK]sigma[grk][TT]*[tt]sqrt(2/T ( [GRK]alpha[grk] ([GRK]tau[grk]1 ((exp(-t/[GRK]tau[grk]1) - 1) [GRK]tau[grk]1/t + 1)) +[BR]",
- " (1-[GRK]alpha[grk]) ([GRK]tau[grk]2 ((exp(-t/[GRK]tau[grk]2) - 1) [GRK]tau[grk]2/t + 1)))),[BR]"
+ "[MATH]f(t) = [GRK]sigma[grk][TT]*[tt][SQRT]2/T ( [GRK]alpha[grk] ([GRK]tau[grk][SUB]1[sub] (([EXP]-t/[GRK]tau[grk][SUB]1[sub][exp] - 1) [GRK]tau[grk][SUB]1[sub]/t + 1)) +[BR]",
+ " (1-[GRK]alpha[grk]) ([GRK]tau[grk][SUB]2[sub] (([EXP]-t/[GRK]tau[grk][SUB]2[sub][exp] - 1) [GRK]tau[grk][SUB]2[sub]/t + 1)))[sqrt][math],[BR]"
"where T is the total time.",
- "[GRK]alpha[grk], [GRK]tau[grk]1 and [GRK]tau[grk]2 are obtained by fitting f^2(t) to error^2.",
+ "[GRK]alpha[grk], [GRK]tau[grk][SUB]1[sub] and [GRK]tau[grk][SUB]2[sub] are obtained by fitting f^2(t) to error^2.",
"When the actual block average is very close to the analytical curve,",
- "the error is [GRK]sigma[grk][TT]*[tt]sqrt(2/T (a [GRK]tau[grk]1 + (1-a) [GRK]tau[grk]2)).",
+ "the error is [MATH][GRK]sigma[grk][TT]*[tt][SQRT]2/T (a [GRK]tau[grk][SUB]1[sub] + (1-a) [GRK]tau[grk][SUB]2[sub])[sqrt][math].",
"The complete derivation is given in",
"B. Hess, J. Chem. Phys. 116:209-217, 2002.[PAR]",
"Option [TT]-g[tt] fits the data to the function given with option",
"[TT]-fitfn[tt].[PAR]",
- "Option [TT]-power[tt] fits the data to b t^a, which is accomplished",
- "by fitting to a t + b on log-log scale. All points after the first",
+ "Option [TT]-power[tt] fits the data to [MATH]b t^a[math], which is accomplished",
+ "by fitting to [MATH]a t + b[math] on log-log scale. All points after the first",
"zero or with a negative value are ignored.[PAR]"
"Option [TT]-luzar[tt] performs a Luzar & Chandler kinetics analysis",
{ "-e", FALSE, etREAL, {&te},
"Last time to read from set" },
{ "-n", FALSE, etINT, {&nsets_in},
- "Read # sets separated by &" },
+ "Read this number of sets separated by &" },
{ "-d", FALSE, etBOOL, {&bDer},
"Use the derivative" },
{ "-dp", FALSE, etINT, {&d},
- "HIDDENThe derivative is the difference over # points" },
+ "HIDDENThe derivative is the difference over this number of points" },
{ "-bw", FALSE, etREAL, {&binwidth},
"Binwidth for the distribution" },
{ "-errbar", FALSE, etENUM, {avbar_opt},
{ "-xydy", FALSE, etBOOL, {&bXYdy},
"Interpret second data set as error in the y values for integrating" },
{ "-regression",FALSE,etBOOL,{&bRegression},
- "Perform a linear regression analysis on the data. If [TT]-xydy[tt] is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize [GRK]chi[grk]^2 = (y - A0 x0 - A1 x1 - ... - AN xN)^2 where now Y is the first data set in the input file and xi the others. Do read the information at the option [TT]-time[tt]." },
+ "Perform a linear regression analysis on the data. If [TT]-xydy[tt] is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize [MATH][GRK]chi[grk]^2 = (y - A[SUB]0[sub] x[SUB]0[sub] - A[SUB]1[sub] x[SUB]1[sub] - ... - A[SUB]N[sub] x[SUB]N[sub])^2[math] where now Y is the first data set in the input file and x[SUB]i[sub] the others. Do read the information at the option [TT]-time[tt]." },
{ "-luzar", FALSE, etBOOL, {&bLuzar},
"Do a Luzar and Chandler analysis on a correlation function and related as produced by [TT]g_hbond[tt]. When in addition the [TT]-xydy[tt] flag is given the second and fourth column will be interpreted as errors in c(t) and n(t)." },
{ "-temp", FALSE, etREAL, {&temp},
- "Temperature for the Luzar hydrogen bonding kinetics analysis" },
+ "Temperature for the Luzar hydrogen bonding kinetics analysis (K)" },
{ "-fitstart", FALSE, etREAL, {&fit_start},
"Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation" },
{ "-fitend", FALSE, etREAL, {&fit_end},
"Time (ps) where to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. Only with [TT]-gem[tt]" },
{ "-smooth",FALSE, etREAL, {&smooth_tail_start},
- "If >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/[GRK]tau[grk])" },
+ "If this value is >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: [MATH]y = A [EXP]-x/[GRK]tau[grk][exp][math]" },
{ "-nbmin", FALSE, etINT, {&nb_min},
"HIDDENMinimum number of blocks for block averaging" },
{ "-resol", FALSE, etINT, {&resol},
"HIDDENResolution for the block averaging, block size increases with"
- " a factor 2^(1/#)" },
+ " a factor 2^(1/resol)" },
{ "-eeexpfit", FALSE, etBOOL, {&bEESEF},
"HIDDENAlways use a single exponential fit for the error estimate" },
{ "-eenlc", FALSE, etBOOL, {&bEENLC},
{ "-eefitac", FALSE, etBOOL, {&bEeFitAc},
"HIDDENAlso plot analytical block average using a autocorrelation fit" },
{ "-filter", FALSE, etREAL, {&filtlen},
- "Print the high-frequency fluctuation after filtering with a cosine filter of length #" },
+ "Print the high-frequency fluctuation after filtering with a cosine filter of this length" },
{ "-power", FALSE, etBOOL, {&bPower},
"Fit data to: b t^a" },
{ "-subav", FALSE, etBOOL, {&bSubAv},
{ "-blen", FALSE, etREAL, {&blen},
"Bond length. By default length of first bond" },
{ "-tol", FALSE, etREAL, {&tol},
- "Half width of distribution as fraction of blen" },
+ "Half width of distribution as fraction of [TT]-blen[tt]" },
{ "-aver", FALSE, etBOOL, {&bAver},
"Average bond length distributions" },
{ "-averdist", FALSE, etBOOL, {&bAverDist},
"The distributions [TT](histo-(dihedral)(RESIDUE).xvg[tt]) are cumulative over all residues of each type.[PAR]",
"If option [TT]-corr[tt] is given, the program will",
"calculate dihedral autocorrelation functions. The function used",
- "is C(t) = < cos([GRK]chi[grk]([GRK]tau[grk])) cos([GRK]chi[grk]([GRK]tau[grk]+t)) >. The use of cosines",
+ "is C(t) = < [COS][GRK]chi[grk]([GRK]tau[grk])[cos] [COS][GRK]chi[grk]([GRK]tau[grk]+t)[cos] >. The use of cosines",
"rather than angles themselves, resolves the problem of periodicity.",
"(Van der Spoel & Berendsen (1997), Biophys. J. 72, 2032-2041).",
"Separate files for each dihedral of each residue",
"rotamers per nanosecond, and the order parameter S^2 of each dihedral.[BR]",
"(d) a table for each residue of the rotamer occupancy.[PAR]",
"All rotamers are taken as 3-fold, except for [GRK]omega[grk] and [GRK]chi[grk] dihedrals",
- "to planar groups (i.e. [GRK]chi[grk]2 of aromatics, Asp and Asn; [GRK]chi[grk]3 of Glu",
- "and Gln; and [GRK]chi[grk]4 of Arg), which are 2-fold. \"rotamer 0\" means ",
+ "to planar groups (i.e. [GRK]chi[grk][SUB]2[sub] of aromatics, Asp and Asn; [GRK]chi[grk][SUB]3[sub] of Glu",
+ "and Gln; and [GRK]chi[grk][SUB]4[sub] of Arg), which are 2-fold. \"rotamer 0\" means ",
"that the dihedral was not in the core region of each rotamer. ",
"The width of the core region can be set with [TT]-core_rotamer[tt][PAR]",
"are equally spaced in time.[PAR]",
"If [TT]-chi_prod[tt] is set (and [TT]-maxchi[tt] > 0), cumulative rotamers, e.g.",
- "1+9([GRK]chi[grk]1-1)+3([GRK]chi[grk]2-1)+([GRK]chi[grk]3-1) (if the residue has three 3-fold ",
+ "1+9([GRK]chi[grk][SUB]1[sub]-1)+3([GRK]chi[grk][SUB]2[sub]-1)+([GRK]chi[grk][SUB]3[sub]-1) (if the residue has three 3-fold ",
"dihedrals and [TT]-maxchi[tt] >= 3)",
"are calculated. As before, if any dihedral is not in the core region,",
"the rotamer is taken to be 0. The occupancies of these cumulative ",
{ "-omega",FALSE, etBOOL, {&bOmega},
"Output for [GRK]omega[grk] dihedrals (peptide bonds)" },
{ "-rama", FALSE, etBOOL, {&bRama},
- "Generate [GRK]phi[grk]/[GRK]psi[grk] and [GRK]chi[grk]1/[GRK]chi[grk]2 Ramachandran plots" },
+ "Generate [GRK]phi[grk]/[GRK]psi[grk] and [GRK]chi[grk][SUB]1[sub]/[GRK]chi[grk][SUB]2[sub] Ramachandran plots" },
{ "-viol", FALSE, etBOOL, {&bViol},
"Write a file that gives 0 or 1 for violated Ramachandran angles" },
{ "-periodic", FALSE, etBOOL, {&bPBC},
{ "-normhisto", FALSE, etBOOL, {&bNormHisto},
"Normalize histograms" },
{ "-ramomega",FALSE,etBOOL, {&bRamOmega},
- "compute average omega as a function of phi/psi and plot it in an [TT].xpm[tt] plot" },
+ "compute average omega as a function of [GRK]phi[grk]/[GRK]psi[grk] and plot it in an [TT].xpm[tt] plot" },
{ "-bfact", FALSE, etREAL, {&bfac_init},
"B-factor value for [TT].pdb[tt] file for atoms with no calculated dihedral order parameter"},
{ "-chi_prod",FALSE,etBOOL, {&bChiProduct},
{ "-nojump", FALSE, etBOOL, {&bNoJump},
"Removes jumps of atoms across the box."},
{ "-eps", FALSE, etREAL, {&eps_rf},
- "Dielectric constant of the surrounding medium. eps=0.0 corresponds to eps=infinity (tin-foil boundary conditions)."},
+ "Dielectric constant of the surrounding medium. The value zero corresponds to infinity (tin-foil boundary conditions)."},
{ "-bfit", FALSE, etREAL, {&bfit},
"Begin of the fit of the straight line to the MSD of the translational fraction of the dipole moment."},
{ "-efit", FALSE, etREAL, {&efit},
"Option [TT]-temp[tt] sets the temperature required for the computation of the static dielectric constant.",
"[PAR]",
"Option [TT]-eps[tt] controls the dielectric constant of the surrounding medium for simulations using",
- "a Reaction Field or dipole corrections of the Ewald summation (eps=0 corresponds to",
+ "a Reaction Field or dipole corrections of the Ewald summation ([TT]-eps[tt]=0 corresponds to",
"tin-foil boundary conditions).",
"[PAR]",
"[TT]-[no]nojump[tt] unfolds the coordinates to allow free diffusion. This is required to get a continuous",
"from the autocorrelation function of the total dipole moment in",
"your simulation. This ACF can be generated by [TT]g_dipoles[tt].",
"The functional forms of the available functions are:[PAR]",
- "One parameter: y = Exp[-a1 x],[BR]",
- "Two parameters: y = a2 Exp[-a1 x],[BR]",
- "Three parameters: y = a2 Exp[-a1 x] + (1 - a2) Exp[-a3 x].[BR]",
+ "One parameter: y = [EXP]-a[SUB]1[sub] x[exp],[BR]",
+ "Two parameters: y = a[SUB]2[sub] [EXP]-a[SUB]1[sub] x[exp],[BR]",
+ "Three parameters: y = a[SUB]2[sub] [EXP]-a[SUB]1[sub] x[exp] + (1 - a[SUB]2[sub]) [EXP]-a[SUB]3[sub] x[exp].[BR]",
"Start values for the fit procedure can be given on the command line.",
"It is also possible to fix parameters at their start value, use [TT]-fix[tt]",
"with the number of the parameter you want to fix.",
"center of mass of the molecule.[PAR]",
"The file [TT]Mtot.xvg[tt] contains the total dipole moment of a frame, the",
"components as well as the norm of the vector.",
- "The file [TT]aver.xvg[tt] contains < |Mu|^2 > and |< Mu >|^2 during the",
+ "The file [TT]aver.xvg[tt] contains < |[GRK]mu[grk]|^2 > and |< [GRK]mu[grk] >|^2 during the",
"simulation.",
"The file [TT]dipdist.xvg[tt] contains the distribution of dipole moments during",
"the simulation",
"dipoles using a first order Legendre polynomial of the angle of the",
"dipole vector and itself a time t later. For this calculation 1001",
"frames will be used. Further, the dielectric constant will be calculated",
- "using an [GRK]epsilon[grk]RF of infinity (default), temperature of 300 K (default) and",
+ "using an [TT]-epsilonRF[tt] of infinity (default), temperature of 300 K (default) and",
"an average dipole moment of the molecule of 2.273 (SPC). For the",
"distribution function a maximum of 5.0 will be used."
};
{ "-mumax", FALSE, etREAL, {&mu_max},
"max dipole in Debye (for histogram)" },
{ "-epsilonRF",FALSE, etREAL, {&epsilonRF},
- "epsilon of the reaction field used during the simulation, needed for dielectric constant calculation. WARNING: 0.0 means infinity (default)" },
+ "[GRK]epsilon[grk] of the reaction field used during the simulation, needed for dielectric constant calculation. WARNING: 0.0 means infinity (default)" },
{ "-skip", FALSE, etINT, {&skip},
"Skip steps in the output (but not in the computations)" },
{ "-temp", FALSE, etREAL, {&temp},
{ visbox },
"HIDDENVisualize a grid of boxes, -1 visualizes the 14 box images" },
{ "-bt", FALSE, etENUM,
- { btype }, "Box type for -box and -d" },
+ { btype }, "Box type for [TT]-box[tt] and [TT]-d[tt]" },
{ "-box", FALSE, etRVEC,
{ newbox }, "Box vector lengths (a,b,c)" },
{ "-angles", FALSE, etRVEC,
{ &dist }, "Distance between the solute and the box" },
{ "-c", FALSE, etBOOL,
{ &bCenter },
- "Center molecule in box (implied by -box and -d)" },
+ "Center molecule in box (implied by [TT]-box[tt] and [TT]-d[tt])" },
{ "-center", FALSE, etRVEC,
{ center }, "Coordinates of geometrical center" },
{ "-aligncenter", FALSE, etRVEC,
"Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file" },
{ "-sig56", FALSE, etREAL,
{ &bSig56 },
- "Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 " },
+ "Use rmin/2 (minimum in the Van der Waals potential) rather than [GRK]sigma[grk]/2 " },
{
"-vdwread", FALSE, etBOOL,
{ &bReadVDW },
- "Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field" },
+ "Read the Van der Waals radii from the file [TT]vdwradii.dat[tt] rather than computing the radii based on the force field" },
{ "-atom", FALSE, etBOOL,
{ &peratom }, "Force B-factor attachment per atom" },
{ "-legend", FALSE, etBOOL,
"calculated ([TT]-etot[tt]).[PAR]",
"An approximation of the free energy can be calculated using:",
- "E(free) = E0 + kT log( <exp((E-E0)/kT)> ), where '<>'",
+ "[MATH]E[SUB]free[sub] = E[SUB]0[sub] + kT [LOG]<[EXP](E-E[SUB]0[sub])/kT[exp]>[log][math], where '<>'",
"stands for time-average. A file with reference free energies",
"can be supplied to calculate the free energy difference",
"with some reference state. Group names (e.g. residue names)",
"will be computed:[BR]",
"Property Energy terms needed[BR]",
"---------------------------------------------------[BR]",
- "Heat capacity Cp (NPT sims): Enthalpy, Temp [BR]",
- "Heat capacity Cv (NVT sims): Etot, Temp [BR]",
+ "Heat capacity C[SUB]p[sub] (NPT sims): Enthalpy, Temp [BR]",
+ "Heat capacity C[SUB]v[sub] (NVT sims): Etot, Temp [BR]",
"Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp[BR]",
"Isothermal compressibility: Vol, Temp [BR]",
"Adiabatic bulk modulus: Vol, Temp [BR]",
"---------------------------------------------------[BR]",
"You always need to set the number of molecules [TT]-nmol[tt].",
- "The Cp/Cv computations do [BB]not[bb] include any corrections",
+ "The C[SUB]p[sub]/C[SUB]v[sub] computations do [BB]not[bb] include any corrections",
"for quantum effects. Use the [TT]g_dos[tt] program if you need that (and you do).[PAR]"
"When the [TT]-viol[tt] option is set, the time averaged",
"violations are plotted and the running time-averaged and",
"With [TT]-fee[tt] an estimate is calculated for the free-energy",
"difference with an ideal gas state: [BR]",
- " [GRK]Delta[grk] A = A(N,V,T) - A_idgas(N,V,T) = kT ln < e^(Upot/kT) >[BR]",
- " [GRK]Delta[grk] G = G(N,p,T) - G_idgas(N,p,T) = kT ln < e^(Upot/kT) >[BR]",
+ " [GRK]Delta[grk] A = A(N,V,T) - A[SUB]idealgas[sub](N,V,T) = kT [LN] < [EXP]U[SUB]pot[sub]/kT[exp] >[ln][BR]",
+ " [GRK]Delta[grk] G = G(N,p,T) - G[SUB]idealgas[sub](N,p,T) = kT [LN] < [EXP]U[SUB]pot[sub]/kT[exp] >[ln][BR]",
"where k is Boltzmann's constant, T is set by [TT]-fetemp[tt] and",
"the average is over the ensemble (or time in a trajectory).",
"Note that this is in principle",
"only correct when averaging over the whole (Boltzmann) ensemble",
"and using the potential energy. This also allows for an entropy",
"estimate using:[BR]",
- " [GRK]Delta[grk] S(N,V,T) = S(N,V,T) - S_idgas(N,V,T) = (<Upot> - [GRK]Delta[grk] A)/T[BR]",
- " [GRK]Delta[grk] S(N,p,T) = S(N,p,T) - S_idgas(N,p,T) = (<Upot> + pV - [GRK]Delta[grk] G)/T",
+ " [GRK]Delta[grk] S(N,V,T) = S(N,V,T) - S[SUB]idealgas[sub](N,V,T) = (<U[SUB]pot[sub]> - [GRK]Delta[grk] A)/T[BR]",
+ " [GRK]Delta[grk] S(N,p,T) = S(N,p,T) - S[SUB]idealgas[sub](N,p,T) = (<U[SUB]pot[sub]> + pV - [GRK]Delta[grk] G)/T",
"[PAR]",
"When a second energy file is specified ([TT]-f2[tt]), a free energy",
- "difference is calculated dF = -kT ln < e ^ -(EB-EA)/kT >A ,",
- "where EA and EB are the energies from the first and second energy",
+ "difference is calculated [BR] dF = -kT [LN]< [EXP]-(E[SUB]B[sub]-E[SUB]A[sub])/kT[exp] >[SUB]A[sub][ln] ,",
+ "where E[SUB]A[sub] and E[SUB]B[sub] are the energies from the first and second energy",
"files, and the average is over the ensemble A. The running average",
"of the free energy difference is printed to a file specified by [TT]-ravg[tt].",
"[BB]Note[bb] that the energies must both be calculated from the same trajectory."
output_env_t oenv;
t_pargs pa[] = {
{ "-box", FALSE, etRVEC, {new_box},
- "box size" },
+ "Box size" },
{ "-nmol", FALSE, etINT , {&nmol_ins},
- "no of extra molecules to insert" },
+ "Number of extra molecules to insert" },
{ "-try", FALSE, etINT , {&nmol_try},
- "try inserting [TT]-nmol[tt] times [TT]-try[tt] times" },
+ "Try inserting [TT]-nmol[tt] times [TT]-try[tt] times" },
{ "-seed", FALSE, etINT , {&seed},
- "random generator seed"},
+ "Random generator seed"},
{ "-vdwd", FALSE, etREAL, {&r_distance},
- "default vdwaals distance"},
+ "Default van der Waals distance"},
{ "-shell", FALSE, etREAL, {&r_shell},
- "thickness of optional water layer around solute" },
+ "Thickness of optional water layer around solute" },
{ "-maxsol", FALSE, etINT, {&max_sol},
- "maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored" },
+ "Maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored" },
{ "-vel", FALSE, etBOOL, {&bReadV},
- "keep velocities from input solute and solvent" }
+ "Keep velocities from input solute and solvent" }
};
CopyRight(stderr,argv[0]);
t_pargs pa[] = {
{ "-fc", FALSE, etRVEC, {fc},
- "force constants (kJ/mol nm^2)" },
+ "Force constants (kJ/mol nm^2)" },
{ "-freeze", FALSE, etREAL, {&freeze_level},
- "if the [TT]-of[tt] option or this one is given an index file will be written containing atom numbers of all atoms that have a B-factor less than the level given here" },
+ "If the [TT]-of[tt] option or this one is given an index file will be written containing atom numbers of all atoms that have a B-factor less than the level given here" },
{ "-disre", FALSE, etBOOL, {&bDisre},
"Generate a distance restraint matrix for all the atoms in index" },
{ "-disre_dist", FALSE, etREAL, {&disre_dist},
{ "-moi", FALSE, etBOOL, {&bMOI},
"Calculate the moments of inertia (defined by the principal axes)." },
{ "-nz", FALSE, etINT, {&nz},
- "Calculate the 2D radii of gyration of # slices along the z-axis" },
+ "Calculate the 2D radii of gyration of this number of slices along the z-axis" },
};
FILE *out;
t_trxstatus *status;
"Take the normal on the membrane in direction X, Y or Z." },
{ "-sl", FALSE, etINT, {&nslices},
"Calculate order parameter as function of boxlength, dividing the box"
- " in #nr slices."}
+ " in this number of slices."}
};
const char *bugs[] = {
"The program assigns whole water molecules to a slice, based on the first "
"Then the following properties are computed:[PAR]",
"[BB]1.[bb] Helix radius (file [TT]radius.xvg[tt]). This is merely the",
"RMS deviation in two dimensions for all C[GRK]alpha[grk] atoms.",
- "it is calced as sqrt((SUM i(x^2(i)+y^2(i)))/N), where N is the number",
+ "it is calculated as [SQRT]([SUM][sum][SUB]i[sub] (x^2(i)+y^2(i)))/N[sqrt] where N is the number",
"of backbone atoms. For an ideal helix the radius is 0.23 nm[BR]",
"[BB]2.[bb] Twist (file [TT]twist.xvg[tt]). The average helical angle per",
"residue is calculated. For an [GRK]alpha[grk]-helix it is 100 degrees,",
"interpolating: 0 corresponds to input structure 1 while",
"1 corresponds to input structure 2.",
"If you specify [TT]-first[tt] < 0 or [TT]-last[tt] > 1 extrapolation will be",
- "on the path from input structure x1 to x2. In general, the coordinates",
- "of the intermediate x(i) out of N total intermidates correspond to:[PAR]",
- "x(i) = x1 + (first+(i/(N-1))*(last-first))*(x2-x1)[PAR]",
+ "on the path from input structure x[SUB]1[sub] to x[SUB]2[sub]. In general, the coordinates",
+ "of the intermediate x(i) out of N total intermediates correspond to:[PAR]",
+ "x(i) = x[SUB]1[sub] + (first+(i/(N-1))*(last-first))*(x[SUB]2[sub]-x[SUB]1[sub])[PAR]",
"Finally the RMSD with respect to both input structures can be computed",
"if explicitly selected ([TT]-or[tt] option). In that case, an index file may be",
"read to select the group from which the RMS is computed."
{ "-ninterm", FALSE, etINT, {&ninterm},
"Number of intermediates" },
{ "-first", FALSE, etREAL, {&first},
- "Corresponds to first generated structure (0 is input x0, see above)" },
+ "Corresponds to first generated structure (0 is input x[SUB]1[sub], see above)" },
{ "-last", FALSE, etREAL, {&last},
- "Corresponds to last generated structure (1 is input x1, see above)" },
+ "Corresponds to last generated structure (1 is input x[SUB]2[sub], see above)" },
{ "-fit", FALSE, etBOOL, {&bFit},
"Do a least squares fit of the second to the first structure before interpolating" }
};
{
{ "-eignr", FALSE, etSTR, {&eignrvec}, "String of eigenvectors to use (first is 1)" },
{ "-phases", FALSE, etSTR, {&phasevec}, "String of phases (default is 0.0)" },
- { "-temp", FALSE, etREAL, {&temp}, "Temperature in Kelvin" },
+ { "-temp", FALSE, etREAL, {&temp}, "Temperature (K)" },
{ "-amplitude", FALSE, etREAL, {&refamplitude}, "Amplitude for modes with eigenvalue<=0" },
{ "-nframes", FALSE, etINT, {&nframes}, "Number of frames to generate" }
};
"Direction of the normal on the membrane" },
{ "-sl", FALSE, etINT, {&nslices},
"Calculate order parameter as function of box length, dividing the box"
- " in #nr slices." },
+ " into this number of slices." },
{ "-szonly", FALSE, etBOOL,{&bSzonly},
"Only give Sz element of order tensor. (axis can be specified with [TT]-d[tt])" },
{ "-unsat", FALSE, etBOOL,{&bUnsat},
"Take the normal on the membrane in direction X, Y or Z." },
{ "-sl", FALSE, etINT, {&nslices},
"Calculate potential as function of boxlength, dividing the box"
- " in #nr slices." } ,
+ " in this number of slices." } ,
{ "-cb", FALSE, etINT, {&cb},
- "Discard first #nr slices of box for integration" },
+ "Discard this number of first slices of box for integration" },
{ "-ce", FALSE, etINT, {&ce},
- "Discard last #nr slices of box for integration" },
+ "Discard this number of last slices of box for integration" },
{ "-tz", FALSE, etREAL, {&fudge_z},
- "Translate all coordinates <distance> in the direction of the box" },
+ "Translate all coordinates by this distance in the direction of the box" },
{ "-spherical", FALSE, etBOOL, {&bSpherical},
"Calculate spherical thingie" },
{ "-ng", FALSE, etINT, {&ngrps},
static real truncate=1000.0;
t_pargs pa[] = {
{ "-t", FALSE, etREAL, {&truncate},
- "trunc distance" },
+ "Groups that are never closer than this distance are not plotted" },
{ "-sep", FALSE, etBOOL, {&bSep},
"Use separate files for each interaction (may be MANY)" }
};
{ "-ttol", FALSE, etREAL, {&ttol},
"Tolerance on time in appropriate units (usually ps)" },
{ "-n", FALSE, etINT, {&nsets_in},
- "Read # sets separated by &" },
+ "Read this number of sets separated by lines containing only an ampersand" },
{ "-d", FALSE, etBOOL, {&bDer},
"Use the derivative" },
{ "-bw", FALSE, etREAL, {&binwidth},
/* { "-cut", bCUTDOWN, etBOOL, {&bCUTDOWN},*/
/* "Display a total cube that is of minimal size" }, */
{ "-bin", FALSE, etREAL, {&rBINWIDTH},
- "Width of the bins in nm" },
+ "Width of the bins (nm)" },
{ "-nab", FALSE, etINT, {&iNAB},
"Number of additional bins to ensure proper memory allocation" }
};
do_view(oenv,fn_tc,"-nxy");
if (fn_cub) {
- fp_cub = xvgropen(fn_cub,"TCAF's and fits", "Time (ps)","TCAF",oenv);
+ fp_cub = xvgropen(fn_cub,"TCAFs and fits", "Time (ps)","TCAF",oenv);
for(kc=0; kc<nkc; kc++) {
fprintf(fp_cub,"%g %g\n",0.0,1.0);
for(i=1; i<ncorr; i++) {
"not independent). For each k-vector the sine and cosine are used, in",
"combination with the velocity in 2 perpendicular directions. This gives",
"a total of 16*2*2=64 transverse currents. One autocorrelation is",
- "calculated fitted for each k-vector, which gives 16 TCAF's. Each of",
- "these TCAF's is fitted to f(t) = exp(-v)(cosh(Wv) + 1/W sinh(Wv)),",
- "v = -t/(2 [GRK]tau[grk]), W = sqrt(1 - 4 [GRK]tau[grk] [GRK]eta[grk]/[GRK]rho[grk] k^2), which gives 16 values of [GRK]tau[grk]",
- "and [GRK]eta[grk]. The fit weights decay with time as exp(-t/wt), and the TCAF and",
- "fit are calculated up to time 5*wt.",
- "The [GRK]eta[grk] values should be fitted to 1 - a [GRK]eta[grk](k) k^2, from which",
+ "calculated fitted for each k-vector, which gives 16 TCAFs. Each of",
+ "these TCAFs is fitted to [MATH]f(t) = [EXP]-v[exp]([COSH]Wv[cosh] + 1/W [SINH]Wv[sinh])[math],",
+ "[MATH]v = -t/(2 [GRK]tau[grk])[math], [MATH]W = [SQRT]1 - 4 [GRK]tau[grk] [GRK]eta[grk]/[GRK]rho[grk] k^2[sqrt][math], which gives 16 values of [GRK]tau[grk]",
+ "and [GRK]eta[grk]. The fit weights decay exponentially with time constant [MATH]w[math] (given with [TT]-wt[tt]) as [MATH][EXP]-t/w[exp][math], and the TCAF and",
+ "fit are calculated up to time [MATH]5*w[math].",
+ "The [GRK]eta[grk] values should be fitted to [MATH]1 - a [GRK]eta[grk](k) k^2[math], from which",
"one can estimate the shear viscosity at k=0.[PAR]",
"When the box is cubic, one can use the option [TT]-oc[tt], which",
- "averages the TCAF's over all k-vectors with the same length.",
- "This results in more accurate tcaf's.",
- "Both the cubic TCAF's and fits are written to [TT]-oc[tt]",
+ "averages the TCAFs over all k-vectors with the same length.",
+ "This results in more accurate TCAFs.",
+ "Both the cubic TCAFs and fits are written to [TT]-oc[tt]",
"The cubic [GRK]eta[grk] estimates are also written to [TT]-ov[tt].[PAR]",
"With option [TT]-mol[tt], the transverse current is determined of",
"molecules instead of atoms. In this case, the index group should",
"consist of molecule numbers instead of atom numbers.[PAR]",
"The k-dependent viscosities in the [TT]-ov[tt] file should be",
- "fitted to [GRK]eta[grk](k) = [GRK]eta[grk]0 (1 - a k^2) to obtain the viscosity at",
+ "fitted to [MATH][GRK]eta[grk](k) = [GRK]eta[grk][SUB]0[sub] (1 - a k^2)[math] to obtain the viscosity at",
"infinite wavelength.[PAR]",
"[BB]Note:[bb] make sure you write coordinates and velocities often enough.",
"The initial, non-exponential, part of the autocorrelation function",
static real wt=5;
t_pargs pa[] = {
{ "-mol", FALSE, etBOOL, {&bMol},
- "Calculate tcaf of molecules" },
+ "Calculate TCAF of molecules" },
{ "-k34", FALSE, etBOOL, {&bK34},
"Also use k=(3,0,0) and k=(4,0,0)" },
{ "-wt", FALSE, etREAL, {&wt},
{ "-multi", FALSE, etINT, {&nmultisim},
"Do multiple simulations in parallel" },
{ "-replex", FALSE, etINT, {&repl_ex_nst},
- "Attempt replica exchange every # steps" },
+ "Attempt replica exchange periodically with this period" },
{ "-reseed", FALSE, etINT, {&repl_ex_seed},
"Seed for replica exchange, -1 is generate a seed" },
{ "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
{
const char *desc[] = {
"[TT]g_vanhove[tt] computes the Van Hove correlation function.",
- "The Van Hove G(r,t) is the probability that a particle that is at r0",
- "at time zero can be found at position r0+r at time t.",
+ "The Van Hove G(r,t) is the probability that a particle that is at r[SUB]0[sub]",
+ "at time zero can be found at position r[SUB]0[sub]+r at time t.",
"[TT]g_vanhove[tt] determines G not for a vector r, but for the length of r.",
"Thus it gives the probability that a particle moves a distance of r",
"in time t.",
"or anisotropic pressure coupling.",
"[PAR]",
"With option [TT]-om[tt] the whole matrix can be written as a function",
- "of t and r or as a function of sqrt(t) and r (option [TT]-sqrt[tt]).",
+ "of t and r or as a function of [SQRT]t[sqrt] and r (option [TT]-sqrt[tt]).",
"[PAR]",
"With option [TT]-or[tt] the Van Hove function is plotted for one",
"or more values of t. Option [TT]-nr[tt] sets the number of times,",
static real sbin=0,rmax=2,rbin=0.01,mmax=0,rint=0;
t_pargs pa[] = {
{ "-sqrt", FALSE, etREAL,{&sbin},
- "Use sqrt(t) on the matrix axis which binspacing # in sqrt(ps)" },
+ "Use [SQRT]t[sqrt] on the matrix axis which binspacing # in sqrt(ps)" },
{ "-fm", FALSE, etINT, {&fmmax},
"Number of frames in the matrix, 0 is plot all" },
{ "-rmax", FALSE, etREAL, {&rmax},
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff