Atom types interchaged on saved dump file while wrapping around a molecule

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1

LAMMPS simulation where I have the following atom types,

Na ion: type 7
O atom of TIP3P water: type 9
H atom : type 8

Below is a part of the LAMMPS output (dump file) for four representative atoms
#lammps
1544 7 0.308291 0.550004 0.930876 0 -1 -1
1545 9 0.428824 0.888473 0.48709 -2 -1 0
1546 8 0.432441 0.882404 0.482596 -2 -1 0
1547 8 0.433352 0.892845 0.478202 -2 -1 0

I want to wrap all atoms around a specific group of atoms and I use the pbc wrap command, in the vmd console as given below

pbc wrap -center com -centersel “resname CNT” -all

after that i save the co-ordinates in lammpstrj file type and part of the saved co-ordinates is as given below

#vmd
1544 9 -9.38336 7.07769 30.9057
1545 7 -0.558907 54.9855 -1.58466
1546 8 -0.294113 54.1265 -1.91368
1547 8 -0.227417 55.6043 -2.23537

here I observed that the atom type 7 and 9 are interchaged as shown above. however the co-ordinates remain same on the files.
Could you suggest, what may be the reason and how to resolve?

Thanks & Regards

2

LAMMPS simulation where I have the following atom types,

Na ion: type 7
O atom of TIP3P water: type 9
H atom : type 8

Below is a part of the LAMMPS output (dump file) for four representative
atoms
#lammps
1544 7 0.308291 0.550004 0.930876 0 -1 -1
1545 9 0.428824 0.888473 0.48709 -2 -1 0
1546 8 0.432441 0.882404 0.482596 -2 -1 0
1547 8 0.433352 0.892845 0.478202 -2 -1 0

I want to wrap all atoms around a specific group of atoms and I use the
pbc wrap command, in the vmd console as given below

pbc wrap -center com -centersel "resname CNT" -all

​this is a VMD not a LAMMPS question. please post it to the vmd-l mailing
list.

axel.​

3

I don’t know about the VMD part, but the LAMMPS
dump command gives you options about dumping
wrapped vs unwrapped coords.

Steve

4

I don't know about the VMD part, but the LAMMPS
dump command gives you options about dumping
wrapped vs unwrapped coords.

​but LAMMPS doesn't allow you to change the center that things are wrapped
around let alone have it be defined as the center of a group or keep
molecules ​intact while wrapping and so on as the pbctools plugin in VMD
does.

axel.