"([TT]-t0[tt] and [TT]-timestep[tt])[BR]",
"[BB]9.[bb] cut the trajectory in small subtrajectories according",
"to information in an index file. This allows subsequent analysis of",
- "the subtrajectories that could, for example be the result of a",
+ "the subtrajectories that could, for example, be the result of a",
"cluster analysis. Use option [TT]-sub[tt].",
"This assumes that the entries in the index file are frame numbers and",
"dumps each group in the index file to a separate trajectory file.[BR]",
"[BB]10.[bb] select frames within a certain range of a quantity given",
"in an [TT].xvg[tt] file.[PAR]",
- "The program [TT]trjcat[tt] can concatenate multiple trajectory files.",
+ "The program [TT]trjcat[tt] is better suited for concatenating multiple trajectory files.",
"[PAR]",
"Currently seven formats are supported for input and output:",
"[TT].xtc[tt], [TT].trr[tt], [TT].trj[tt], [TT].gro[tt], [TT].g96[tt],",
"No checks are performed to ensure integrity",
"of the resulting combined trajectory file.[PAR]",
"Option [TT]-sep[tt] can be used to write every frame to a separate",
- ".gro, .g96 or .pdb file, default all frames all written to one file.",
+ "[TT].gro, .g96[tt] or [TT].pdb[tt] file. By default, all frames all written to one file.",
"[TT].pdb[tt] files with all frames concatenated can be viewed with",
"[TT]rasmol -nmrpdb[tt].[PAR]",
"It is possible to select part of your trajectory and write it out",
"We recommend to use the portable [TT].xtc[tt] format for your analysis",
"to save disk space and to have portable files.[PAR]",
"There are two options for fitting the trajectory to a reference",
- "either for essential dynamics analysis or for whatever.",
+ "either for essential dynamics analysis, etc.",
"The first option is just plain fitting to a reference structure",
- "in the structure file, the second option is a progressive fit",
+ "in the structure file. The second option is a progressive fit",
"in which the first timeframe is fitted to the reference structure ",
"in the structure file to obtain and each subsequent timeframe is ",
"fitted to the previously fitted structure. This way a continuous",
"conformational transitions.[PAR]",
"Option [TT]-pbc[tt] sets the type of periodic boundary condition",
"treatment:[BR]",
- "* [TT]mol[tt] puts the center of mass of molecules in the box.[BR]",
- "* [TT]res[tt] puts the center of mass of residues in the box.[BR]",
- "* [TT]atom[tt] puts all the atoms in the box.[BR]",
- "* [TT]nojump[tt] checks if atoms jump across the box and then puts",
+ "[TT]* mol[tt] puts the center of mass of molecules in the box.[BR]",
+ "[TT]* res[tt] puts the center of mass of residues in the box.[BR]",
+ "[TT]* atom[tt] puts all the atoms in the box.[BR]",
+ "[TT]* nojump[tt] checks if atoms jump across the box and then puts",
"them back. This has the effect that all molecules",
"will remain whole (provided they were whole in the initial",
- "conformation), note that this ensures a continuous trajectory but",
+ "conformation). [BB]Note[bb] that this ensures a continuous trajectory but",
"molecules may diffuse out of the box. The starting configuration",
"for this procedure is taken from the structure file, if one is",
"supplied, otherwise it is the first frame.[BR]",
- "* [TT]cluster[tt] clusters all the atoms in the selected index",
- "such that they are all closest to the center of mass of the cluster",
- "which is iteratively updated. Note that this will only give meaningful",
+ "[TT]* cluster[tt] clusters all the atoms in the selected index",
+ "such that they are all closest to the center of mass of the cluster,",
+ "which is iteratively updated. [BB]Note[bb] that this will only give meaningful",
"results if you in fact have a cluster. Luckily that can be checked",
"afterwards using a trajectory viewer. Note also that if your molecules",
"are broken this will not work either.[BR]",
- "* [TT]whole[tt] only makes broken molecules whole.[PAR]",
+ "[TT]* whole[tt] only makes broken molecules whole.[PAR]",
"Option [TT]-ur[tt] sets the unit cell representation for options",
"[TT]mol[tt], [TT]res[tt] and [TT]atom[tt] of [TT]-pbc[tt].",
"All three options give different results for triclinic boxes and",
"[TT]tric[tt] is the triclinic unit cell.",
"[TT]compact[tt] puts all atoms at the closest distance from the center",
"of the box. This can be useful for visualizing e.g. truncated",
- "octahedrons. The center for options [TT]tric[tt] and [TT]compact[tt]",
+ "octahedra. The center for options [TT]tric[tt] and [TT]compact[tt]",
"is [TT]tric[tt] (see below), unless the option [TT]-boxcenter[tt]",
"is set differently.[PAR]",
"Option [TT]-center[tt] centers the system in the box. The user can",
"[TT]zero[tt]: zero.",
"Use option [TT]-pbc mol[tt] in addition to [TT]-center[tt] when you",
"want all molecules in the box after the centering.[PAR]",
- "With [TT]-dt[tt] it is possible to reduce the number of ",
+ "With [TT]-dt[tt], it is possible to reduce the number of ",
"frames in the output. This option relies on the accuracy of the times",
"in your input trajectory, so if these are inaccurate use the",
"[TT]-timestep[tt] option to modify the time (this can be done",
- "simultaneously). For making smooth movies the program [TT]g_filter[tt]",
+ "simultaneously). For making smooth movies, the program [TT]g_filter[tt]",
"can reduce the number of frames while using low-pass frequency",
"filtering, this reduces aliasing of high frequency motions.[PAR]",
"Using [TT]-trunc[tt] trjconv can truncate [TT].trj[tt] in place, i.e.",
"without copying the file. This is useful when a run has crashed",
- "during disk I/O (one more disk full), or when two contiguous",
- "trajectories must be concatenated without have double frames.[PAR]",
- "[TT]trjcat[tt] is more suitable for concatenating trajectory files.[PAR]",
+ "during disk I/O (i.e. full disk), or when two contiguous",
+ "trajectories must be concatenated without having double frames.[PAR]",
"Option [TT]-dump[tt] can be used to extract a frame at or near",
"one specific time from your trajectory.[PAR]",
"Option [TT]-drop[tt] reads an [TT].xvg[tt] file with times and values.",
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff