用VMD转换data文件
convert.tcl
package require topotools
package require pbctools
## Select atoms and asign info
set atomS [atomselect top {name S}]
$atomS set mass 80
$atomS set charge -1
$atomS set radius 1.7
$atomS set name S
$atomS set type Qa
#$atomS delete
## guess bonding from atomic radii
mol bondsrecalc top
## resets all bond types
topo clearbonds
topo clearangles
topo guessbonds
topo guessangles
topo retypebonds
topo retypeangles
## check info and output
mol reanalyze top
pbc set {50.0 50.0 50.0 90.0 90.0 90.0}
topo writelammpsdata data.poly1B
#topo readlammpsdata data.poly100B
显示
超出周期性box
pbc wrap -compound res -all
pbc box
参考：
- TopoTool-Tutorial - Part 1
- water molecules out of box boundary
- lammps建模方法，即生成data文件
- TopoTools Command
- [lammps-users] bond-angle-Dihedral Coeffs
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