-misc-misplaced-widening-cast,-readability-named-parameter,\
-misc-suspicious-string-compare,\
-performance-unnecessary-value-param,\
- -misc-suspicious-missing-comma,\
-misc-misplaced-const,\
-misc-incorrect-roundings,-misc-macro-parentheses,-readability-function-size,-readability-else-after-return,\
-readability-inconsistent-declaration-parameter-name,-misc-throw-by-value-catch-by-reference,\
"x", "v", "sdx-unsupported", "CGp", "LD-rng-unsupported", "LD-rng-i-unsupported",
"disre_initf", "disre_rm3tav",
"orire_initf", "orire_Dtav",
- "svir_prev", "nosehoover-vxi", "v_eta", "vol0", "nhpres_xi", "nhpres_vxi", "fvir_prev", "fep_state", "MC-rng-unsupported", "MC-rng-i-unsupported"
+ "svir_prev", "nosehoover-vxi", "v_eta", "vol0", "nhpres_xi", "nhpres_vxi", "fvir_prev", "fep_state", "MC-rng-unsupported", "MC-rng-i-unsupported",
"barostat-integral"
};
"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]"
+ "zero or with a negative value are ignored.[PAR]",
"Option [TT]-luzar[tt] performs a Luzar & Chandler kinetics analysis",
"on output from [gmx-hbond]. The input file can be taken directly",
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"dielectric constant. To obtain a reasonable result, the index group has to be neutral.",
"Furthermore, the routine is capable of extracting the static conductivity from the current ",
"autocorrelation function, if velocities are given. Additionally, an Einstein-Helfand fit ",
- "can be used to obtain the static conductivity."
+ "can be used to obtain the static conductivity.",
"[PAR]",
"The flag [TT]-caf[tt] is for the output of the current autocorrelation function and [TT]-mc[tt] writes the",
"correlation of the rotational and translational part of the dipole moment in the corresponding",
"in the trajecotry with sufficiently high frequency such as to cover",
"all vibrations. For flexible systems that would be around a few fs",
"between saving. Properties based on the DoS are printed on the",
- "standard output."
+ "standard output.",
"Note that the density of states is calculated from the mass-weighted",
"autocorrelation, and by default only from the square of the real",
"component rather than absolute value. This means the shape can differ",
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"in the index file. The distance R is calculated on the basis of",
"the COMs of the given atom pairs.",
"The [TT]-pbcdist[tt] option calculates distances to the nearest periodic",
- "image instead to the distance in the box. This works however only,"
+ "image instead to the distance in the box. This works however only,",
"for periodic boundaries in all 3 dimensions.",
"The [TT]-norm[tt] option (area-) normalizes the histograms."
};
"",
"You always need to set the number of molecules [TT]-nmol[tt].",
"The C[SUB]p[sub]/C[SUB]v[sub] computations do [BB]not[bb] include any corrections",
- "for quantum effects. Use the [gmx-dos] program if you need that (and you do).[PAR]"
+ "for quantum effects. Use the [gmx-dos] program if you need that (and you do).[PAR]",
"Option [TT]-odh[tt] extracts and plots the free energy data",
"(Hamiltoian differences and/or the Hamiltonian derivative dhdl)",
"n(t) can be defined as either all pairs that are not within contact distance r at time t",
"(corresponding to leaving the -r2 option at the default value 0) or all pairs that",
"are within distance r2 (corresponding to setting a second cut-off value with option -r2).",
- "See mentioned literature for more details and definitions."
+ "See mentioned literature for more details and definitions.",
"[PAR]",
/* "It is also possible to analyse specific hydrogen bonds with",
"[THISMODULE] computes the tetrahedrality order parameters around a ",
"given atom. Both angle an distance order parameters are calculated. See",
"P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.",
- "for more details.[PAR]"
+ "for more details.[PAR]",
"[THISMODULE] calculates the order parameter in a 3d-mesh in the box, and",
"with 2 phases in the box gives the user the option to define a 2D interface in time",
"separating the faces by specifying parameters [TT]-sgang1[tt] and",
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"order tensor component (specified by the [TT]-d[tt] option) is given and the",
"order parameter per slice is calculated as well. If [TT]-szonly[tt] is not",
"selected, all diagonal elements and the deuterium order parameter is",
- "given.[PAR]"
+ "given.[PAR]",
"The tetrahedrality order parameters can be determined",
"around an atom. Both angle an distance order parameters are calculated. See",
"P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.",
"if using the sPME algorithm. The flag [TT]-tune[tt] will determine",
"the splitting parameter such that the error is equally",
"distributed over the real and reciprocal space part.",
- "The part of the error that stems from self interaction of the particles "
+ "The part of the error that stems from self interaction of the particles ",
"is computationally demanding. However, a good a approximation is to",
"just use a fraction of the particles for this term which can be",
"indicated by the flag [TT]-self[tt].[PAR]",
"deviation (RMSD), the size-independent [GRK]rho[grk] similarity parameter",
"([TT]rho[tt]) or the scaled [GRK]rho[grk] ([TT]rhosc[tt]), ",
"see Maiorov & Crippen, Proteins [BB]22[bb], 273 (1995).",
- "This is selected by [TT]-what[tt].[PAR]"
+ "This is selected by [TT]-what[tt].[PAR]",
"Each structure from a trajectory ([TT]-f[tt]) is compared to a",
"reference structure. The reference structure",
"[THISMODULE] computes SANS spectra using Debye formula.",
"It currently uses topology file (since it need to assigne element for each atom).",
"[PAR]",
- "Parameters:[PAR]"
+ "Parameters:[PAR]",
"[TT]-pr[tt] Computes normalized g(r) function averaged over trajectory[PAR]",
"[TT]-prframe[tt] Computes normalized g(r) function for each frame[PAR]",
"[TT]-sq[tt] Computes SANS intensity curve averaged over trajectory[PAR]",
"[REF].tpr[ref] file; the last test (number [TT]ntpr[tt]) will have the Coulomb cutoff",
"specified by [TT]-rmax[tt] with a somewhat smaller PME grid at the same time. ",
"In this last test, the Fourier spacing is multiplied with [TT]rmax[tt]/rcoulomb. ",
- "The remaining [REF].tpr[ref] files will have equally-spaced Coulomb radii (and Fourier "
+ "The remaining [REF].tpr[ref] files will have equally-spaced Coulomb radii (and Fourier ",
"spacings) between these extremes. [BB]Note[bb] that you can set [TT]-ntpr[tt] to 1",
"if you just seek the optimal number of PME-only ranks; in that case",
"your input [REF].tpr[ref] file will remain unchanged.[PAR]",
"are by default reset after 100 steps. For large systems (>1M atoms), as well as ",
"for a higher accuracy of the measurements, you should set [TT]-resetstep[tt] to a higher value.",
"From the 'DD' load imbalance entries in the md.log output file you",
- "can tell after how many steps the load is sufficiently balanced. Example call:[PAR]"
+ "can tell after how many steps the load is sufficiently balanced. Example call:[PAR]",
"[TT]gmx tune_pme -np 64 -s protein.tpr -launch[tt][PAR]",
"After calling [gmx-mdrun] several times, detailed performance information",
"is available in the output file [TT]perf.out[tt].",
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"of molecule numbers instead of atom numbers.[PAR]",
"By using option [TT]-os[tt] you can also extract the estimated",
"(vibrational) power spectrum, which is the Fourier transform of the",
- "velocity autocorrelation function."
+ "velocity autocorrelation function.",
"Be sure that your trajectory contains frames with velocity information",
"(i.e. [TT]nstvout[tt] was set in your original [REF].mdp[ref] file),",
"and that the time interval between data collection points is",
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
" From the pull force the position in the umbrella potential is",
" computed. This does not work with tabulated umbrella potentials.",
"* With option [TT]-ip[tt], the user provides file names of (gzipped) [REF].pdo[ref] files, i.e.",
- " the GROMACS 3.3 umbrella output files. If you have some unusual"
+ " the GROMACS 3.3 umbrella output files. If you have some unusual",
" reaction coordinate you may also generate your own [REF].pdo[ref] files and",
" feed them with the [TT]-ip[tt] option into to [THISMODULE]. The [REF].pdo[ref] file header",
" must be similar to the following::",
"interactions can be kept by turning off [TT]-rmvsbds[tt]. Additionally,",
"all constraints for distances which will be constant anyway because",
"of virtual site constructions will be removed. If any constraints remain",
- "which involve virtual sites, a fatal error will result.[PAR]"
+ "which involve virtual sites, a fatal error will result.[PAR]",
"To verify your run input file, please take note of all warnings",
"on the screen, and correct where necessary. Do also look at the contents",
"in a file called [TT]grompp.log[tt] (along with real debug info). You",
"can see the contents of the run input file with the [gmx-dump]",
"program. [gmx-check] can be used to compare the contents of two",
- "run input files.[PAR]"
+ "run input files.[PAR]",
"The [TT]-maxwarn[tt] option can be used to override warnings printed",
"by [THISMODULE] that otherwise halt output. In some cases, warnings are",
"(default=5) of any position in [TT]POS_EXPR[tt] as seen from [TT]POS[tt]",
"a position expression that evaluates to a single position), i.e., atoms",
"in the solid angle spanned by the positions in [TT]POS_EXPR[tt] and",
- "centered at [TT]POS[tt].[PAR]"
+ "centered at [TT]POS[tt].[PAR]",
"Technically, the solid angle is constructed as a union of small cones",
"whose tip is at [TT]POS[tt] and the axis goes through a point in",
"run input files this way, the default relative tolerance is reduced",
"to 0.000001 and the absolute tolerance set to zero to find any differences",
"not due to minor compiler optimization differences, although you can",
- "of course still set any other tolerances through the options."
+ "of course still set any other tolerances through the options.",
"Similarly a pair of trajectory files can be compared (using the [TT]-f2[tt]",
"option), or a pair of energy files (using the [TT]-e2[tt] option).[PAR]",
"For free energy simulations the A and B state topology from one",
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff