Tools and information for AMBER and CPPTRAJ examples
Updated: March 25, 2019
Alternative translational diffusion calculation which can calculate diffusion in specified regions. stfcdiffusion mask <mask> [out <file>] [time <time per frame>] [mask2 <mask>] [lower <distance>] [upper <distance>] [nwout <file>]) [avout <file>] [distances] [com] [x|y|z|xy|xz|yz|xyz] mask <mask> Atoms for which… Read More
Updated: March 25, 2019
SPAM method for estimating relative free energies of waters in hydration shell around proteins. spam <filename> [solv <solvname>] [reorder] [name <name>] [purewater] [cut <cut>] [info <infofile>] [summary <summary>] [site_size <size>] [sphere] [out <datafile>] [dgbulk <dgbulk>] [dhbulk <dhbulk>] [temperature… Read More
Updated: March 25, 2019
Set velocities for specified atoms using Maxwellian distribution based on given temperature. setvelocity [<mask>] [tempi <temperature>] [ig <random seed>] [<mask>] Mask of atoms to assign velocities to. [tempi <temperature>] Assign velocities at specified temperature (default 300.0 K). [ig… Read More
Updated: March 25, 2019
Scale coordinates in X/Y/Z directions by specified factors. scale x <sx> y <sy> z <sz> <mask> Scale the X|Y|Z coordinates of atoms in <mask> by <sx>|<sy>|<sz>.
Updated: March 25, 2019
Calculate the running average of coordinates over specified window size. runavg [window <window_size>] Note that for backwards compatibility with ptraj runningaverage is also accepted. Replaces the current frame with a running average over a number of frames specified… 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
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