Hello everyone,
I’m a brazilian undergraduate student in the phisics program of the University of São Paulo, Brazil and work in a project where I use VR to improve scientists intuition about nanometric systems. For this project, now I need pdb output from a LAMMPS simulation. More specifically, I need to use iMD in a different program (non-VMD) and this program only read pdb files.
I found molfile plugin in LAMMPS but I have some trouble with that. My actual problem is related to LAMMPS dump molfile output which doesn’t write neither the molecule type (e.g.: Oxigen, Hidrogen, etc.) nor the bond info (the atoms seem to be separated and not bonded as they should be). Actually, I don’t know how to change these infos in LAMMPS input file (in.something), could you help me with this task, please?
My actual output for a simple water model is shown in the image below.
Thanks for your attention and help,
Lauro B. Braz.
Área de anexos
Hello everyone,
I'm a brazilian undergraduate student in the phisics program of the University of São Paulo, Brazil and work in a project where I use VR to improve scientists intuition about nanometric systems. For this project, now I need pdb output from a LAMMPS simulation. More specifically, I need to use iMD in a different program (non-VMD) and this program only read pdb files.
I found molfile plugin in LAMMPS but I have some trouble with that. My actual problem is related to LAMMPS dump molfile output which doesn't write neither the molecule type (e.g.: Oxigen, Hidrogen, etc.) nor the bond info (the atoms seem to be separated and not bonded as they should be). Actually, I don't know how to change these infos in LAMMPS input file (in.something), could you help me with this task, please?
have you looked at the dump_modify command? please also note, that the
dump molfile style can only output data, that is available internally,
and LAMMPS does not use many of the fields that are present in PDB
files, so it is impossible to output a complete and fully compliant
file.
two more general remaks.
1) you may find it much easier to generate a suitable pdb file from a
regular dump file using VMD and a little scripting. please note, that
for IMD, you only need a starting geometry, the rest is communicated
via the IMD API
2) PDB files do not store topology information for known residues.
CONECT records are only applicable for HETAM entries to represent
unknown residues. simulation software typically obtains topology
information from specific topology file formats, e.g. .psf files in
case of CHARMM/NAMD/Xplor. VMD usually guesses bonds based on atom
types, but for that you have to feed VMD the correct information, and
LAMMPS - by default - does not provide it. you have to use customized
dumps with element information included for VMD to recognize the
elements (LAMMPS doesn't care about those and also doesn't use string
based atom type force field matching, which only makes sense for some
force fields) and thus also use correct heuristics to detect expected
bonds.
axel.