Client No Solvent

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A command-line interface for Molecular Dynamics Analysis routines.

version: 0.11.2

Remove solvent from trajectory.

Algorithm

Removes solvent from trajectory using MDTraj.remove_solvent.

Examples

Remove all solvent:

taurenmd nosol top.pdb traj.dcd -d traj_nosol.dcd -o

Remove all solvent except for NA atoms:

taurenmd nosol top.pdb traj.dcd -d traj_nosolNA.dcd -e Na -o

tmdnosol can be used as main command:

tmdnosol [...]

References

• MD data accessed and/or processed using MDTraj

usage: tmdnosol [-h] [-v] [-i] [-d TRAJ_OUTPUT] [-o [TOP_OUTPUT]]
                [-m MAINTAIN [MAINTAIN ...]]
                topology trajectories [trajectories ...]

Positional Arguments

topology

Path to the topology file.

trajectories

Path to the trajectory files. If multiple files are given, trajectories will be concatenated by input order.

Named Arguments

-v, --version

show program’s version number and exit

-i, --insort

Sorts input trajectories paths according to their tail numbers, if paths are formatted as follows: my_trajectory_#.dcd, where # is a number. Defaults to False.

Default: False

-d, --traj-output

Modified trajectory output file name. File type will be defined by file name extension. Defaults to traj_out.dcd.

Default: “traj_out.dcd”

-o, --top-output

Export edited trajectory first frame as topololy file. You can specify the exact file name, otherwise, defaults to input trajectory path + ‘frame0.pdb’. Also, if name starts with ‘’, it is used as file suffix, if name ends with ‘_’, it is used as prefix, instead.

Default: False

-m, --maintain

List of solvent residue names to maintain in trajectory. Feeds MDTraj.Trajectory.remove_solvent.exclude parameter.