rotate
Rotate the system around X/Y/Z axes, a specified axis, or via given rotation matrices. rotate [<mask>] { [x <xdeg>] [y <ydeg>] [z <zdeg>] | axis0 <mask0> axis1 <mask1> <deg> | usedata <set name> [inverse] } [<mask>] Rotate atoms… Read More
Updated: March 25, 2019
Rotate the system around X/Y/Z axes, a specified axis, or via given rotation matrices. rotate [<mask>] { [x <xdeg>] [y <ydeg>] [z <zdeg>] | axis0 <mask0> axis1 <mask1> <deg> | usedata <set name> [inverse] } [<mask>] Rotate atoms… Read More
Updated: March 26, 2019
Replicate unit cell in specified (or all) directions for specfied atoms and write to trajectory. replicatecell [out <traj filename>] [parmout <parm filename>] [name <dsname>] { all | dir <XYZ> [dir <XYZ> …] } [<mask>] out <traj filename> Write… Read More
Updated: March 26, 2019
Swap specified ions with randomly selected solvent molecules. randomizeions <mask> [around <mask> by <distance>] [overlap <value>] [noimage] [seed <value>] This can be used to randomly swap the positions of solvent and single atom ions. The “overlap” specifies the… Read More
Updated: March 26, 2019
Calculate radius of gyration (and optionally tensor) for specified atoms. radgyr [name>] [<mask>] [out <filename>] [mass] [nomax] [tensor] [<name>] Data set name. [<mask>] Atoms to calculate radius of gyration for; default all atoms. [out <filename>] Write data to… Read More
Updated: March 26, 2019
Calculate ring pucker using five or six points. pucker [<name>] <mask1> <mask2> <mask3> <mask4> <mask5> [<mask6>] [geom] [out <filename>] [altona | cremer] [amplitude] [theta] [range360] [offset <offset>] <name> Output data set name. <maskX> Five (optionally six) atom masks… Read More
Updated: March 26, 2019
Project coordinates along given eigenvectors. projection [<name>] evecs <dataset name> [out <outfile>] [beg <beg>] [end <end>] [<mask>] [dihedrals <dataset arg>] [start <start>] [stop <stop>] [offset <offset>] [<name>] Output data set name. evecs <dataset name> Data set containing eigenvectors… Read More
Updated: March 26, 2019
Calculate and optionally align system along principal axes. principal [<mask>] [dorotation] [out <filename>] [name <dsname>] [<mask>] Mask of atoms used to determine principal axes (default all). [dorotation] Align coordinates along principal axes. [out <filename>] Write resulting eigenvalues/eigenvectors to… Read More
Updated: March 26, 2019
Calculate pair-wise non-bonded energies. pairwise [<name>] [<mask>] [out <filename>] [cuteelec <ecut>] [cutevdw <vcut>] [ reference | ref <name> | refindex <#> ] [cutout <cut mol2 prefix>] [vmapout <vdw map>] [emapout <elec map>] [avgout <avg file>] [eout <eout file>]… Read More
Updated: March 26, 2019
Calculate pair distribution function. pairdist out <filename> mask <mask> [delta <resolution>] Calculate pair distribution function. In the following, defaults are given in parentheses. The out keyword specifies output file for histogram: distance, P(r), s(P(r)). The mask option specifies… Read More
Updated: December 17, 2019
Write frames to a trajectory file within a list of Actions. outtraj <filename> [ trajout args ][maxmin <dataset> min <min> max <max>] <filename> Output trajectory file name. [trajout args] Output trajectory arguments (see the trajout command). [maxmin <dataset>… Read More
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