hi dear
when I dump my MD to vmd , I face with a lot of extra bonding between the atoms especially the H2O atoms it is like with a lot of lines that damage my view . My dump command is …
dump 3 all custom 50000 equilib-0.lammpstrj id type x y z vx vy vz
best
ramin
hi dear
when I dump my MD to vmd , I face with a lot of extra bonding between the
please note that this is more of a VMD question than a LAMMPS question
and thus would be better directed there.
atoms especially the H2O atoms it is like with a lot of lines that damage my
view . My dump command is ...
there are two steps that you can do.
1) import the bonding pattern from your data file to VMD using the
topotools plugin:
http://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-readlammpsdata-file-name-atom-style
if you then run: topo guessatoms lammps data
it should also change the atom names and radii to match the elements,
provided you set the proper masses in the data file.
dump 3 all custom 50000 equilib-0.lammpstrj id type x y z vx vy vz
change this to
dump 3 all custom 50000 equilib-0.lammpstrj id type xu yu zu vx vy vz
or if you need to keep for some reason the wrapped coordinates
dump 3 all custom 50000 equilib-0.lammpstrj id type x y z vx
vy vz ix iy iz
this will avoid the wrapping of atom coordinates back into the
principle unit cell.
if you want to do wrapping on the base of whole molecules, you can then do that
as a postprocessing step inside of VMD using the pbctool plugin with
pbc wrap -compound fragment -all
axel.