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MD configuration making tools
Python Tcl Shell
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README
arrange-radial.tcl
arrange.tcl
distance.tcl
makeMol.py
makePoints.py
makeSpherePoints.py
make_dmu-mixed.tcl
mol_man.tcl
prep-sphere.sh
prep.sh

README

1.Use makeMol.py to make and duplicate the molecule (in a gro file) into another gro file,
  Note that normally the orinigal gro files should contain only one molecule per file
2.Use editconf to format the ini.gro 
3.Use makePoints.py to create a position.xyz file containing the desired position coordinates in each line
4.Use arrange.tcl to arrange those molecules in ini.gro onto the corresponding positions in position.xyz

An example of the workflow is given in the prep.sh

A similar procedure for arranging molecules on a sphere is provided in prep-sphere.sh
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