Dear all,
I used this command “dump 1 water custom 100 water.lammpstrj id mol type x y z”to get the trajectories of water molecules. Then loading the trajectory file into VMD, but the hydrogen bonds are not shown when selecting the drawing method “HBonds”. It seems like that VMD doesn’t recognize the oxygen and hydrogen atoms. Do you know which style and args should I use for reorganizing the Hbonds ?
Jessica
Dear all,
I used this command “dump 1 water custom 100 water.lammpstrj id mol type x y z”to get the trajectories of water molecules. Then loading the trajectory file into VMD, but the hydrogen bonds are not shown when selecting the drawing method "HBonds". It seems like that VMD doesn't recognize the oxygen and hydrogen atoms. Do you know which style and args should I use for reorganizing the Hbonds ?
how should VMD recognize this, when you do not provide any suitable
information? all you tell VMD with your dump file is, that you have
atoms of type 1 and type 2 and so on. how can VMD know what those
types stand for. you can try to include the element field and use
dump_modify to set a mapping between numerical atom types and elements
(i.e. atom names).
you may find it much easier, however, to just load one trajectory
frame or your data file into VMD and then use VMD/Tcl scripting to set
all the properties to suitable text values (atom names, atom types,
residue name, sequence etc.) and then save the result as a .psf file.
for as long as you don't change number or order of atom ids, you can
load this psf file first before reading coordinate data and VMD will
work fine. this is how VMD is designed for (in NAMD/CHARMM one uses a
.psf file plus .dcd files, which contain coordinates and box
information only).
for more detailed discussion, please carefully study the VMD user's
guide and please direct questions about details for how to use VMD
scripting to the VMD mailing list.
axel.
axel.