int gmx_trjconv(int argc, char *argv[])
{
const char *desc[] = {
- "[THISMODULE] can convert trajectory files in many ways:[BR]",
- "* from one format to another[BR]",
- "* select a subset of atoms[BR]",
- "* change the periodicity representation[BR]",
- "* keep multimeric molecules together[BR]",
- "* center atoms in the box[BR]",
- "* fit atoms to reference structure[BR]",
- "* reduce the number of frames[BR]",
- "* change the timestamps of the frames ([TT]-t0[tt] and [TT]-timestep[tt])[BR]",
- "[TT]*[tt] 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",
- "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]",
- "[TT]*[tt] select frames within a certain range of a quantity given",
- "in an [REF].xvg[ref] file.[PAR]",
-
+ "[THISMODULE] can convert trajectory files in many ways:",
+ "",
+ "* from one format to another",
+ "* select a subset of atoms",
+ "* change the periodicity representation",
+ "* keep multimeric molecules together",
+ "* center atoms in the box",
+ "* fit atoms to reference structure",
+ "* reduce the number of frames",
+ "* change the timestamps of the frames ([TT]-t0[tt] and [TT]-timestep[tt])",
+ "* 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",
+ " 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.",
+ "* select frames within a certain range of a quantity given",
+ " in an [REF].xvg[ref] file.",
+ "",
"[gmx-trjcat] is better suited for concatenating multiple trajectory files.",
"[PAR]",
"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,",
- "and requires a run input file to be supplied with [TT]-s[tt].[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). [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. [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]",
- "The separate option [TT]-clustercenter[tt] can be used to specify an",
- "approximate center for the cluster. This is useful e.g. if you have",
- "two big vesicles, and you want to maintain their relative positions.[BR]",
- "[TT]* whole[tt] only makes broken molecules whole.[PAR]",
+ "treatment:",
+ "",
+ " * [TT]mol[tt] puts the center of mass of molecules in the box,",
+ " and requires a run input file to be supplied with [TT]-s[tt].",
+ " * [TT]res[tt] puts the center of mass of residues in the box.",
+ " * [TT]atom[tt] puts all the atoms in the box.",
+ " * [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). [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.",
+ " * [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.",
+ "",
+ " The separate option [TT]-clustercenter[tt] can be used to specify an",
+ " approximate center for the cluster. This is useful e.g. if you have",
+ " two big vesicles, and you want to maintain their relative positions.",
+ " * [TT]whole[tt] only makes broken molecules whole.",
+ "",
"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].",
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff