dear all
Can anyone tell me how to assign the partial charge for each atom in a hetero atomic system? Actually i need to introduce the charge column in the coordinate file, so i can use the ‘set’ command in lammps to assign charge for each atom type…otherwise it says “incorrect atom format in data file” when i use the command(set atom 1 charge 0.43) without the charge column in data file …
thanku
You probably need to use atom_style charge if you want atoms to have charges.
http://lammps.sandia.gov/doc/atom_style.html
Anders
Dear all
I am using VMD to generate the input data file for my simulation which contains solvated graphene. But the problem is when I generate the data file using the command (topo writelammpsdata) in VMD, it assigns only the number of bond and number of atoms, it does not give any info about the bond angle, dihedral or improper. So my question is how one can assign the angles, dihedrals and their types in LAMMPS data file?
thank you
Dear all
I am using VMD to generate the input data file for my simulation which
contains solvated graphene. But the problem is when I generate the data
file using the command (topo writelammpsdata) in VMD, it assigns only the
number of bond and number of atoms, it does not give any info about the
bond angle, dihedral or improper. So my question is how one can assign the
angles, dihedrals and their types in LAMMPS data file?
you process of creating the data file is incomplete. the writelammpsdata
function of the VMD TopoTools plugin will not do any automatic atom typing,
partial charge assignment, or topology creation or any other necessary
operation required by a force field. it relies instead *completely* on data
that is available inside VMD. this is deliberate, because the actual rules
for how to assign force field parameters or how to type atoms vary between
force field. thus in almost all cases, some more or less complex VMD/Tcl
scripting is required to build/assign/derive the necessary information
inside VMD before you would write it out. this requires understanding the
particular force field you are using and understanding the various script
operations that VMD supports. some of the more complex operations required
for that are available as functions inside the TopoTools plugin. Please
study the TopoTools documentation and the VMD User's Guide section about
Tcl scripting carefully. Please also review the TopoTools tutorial pages on
my home page to see examples for how this can be implemented. It also shows
how VMD heuristic guesses can be wrong and corrected through scripting and
how missing information can be created, in particular for the OPLS/AA force
field, which has simple increment rules for assigning partial charges
unlike other force fields, that require importing information from a
database of residues/fragments. in the latter case, e.g. for CHARMM, the
"native" topology building tools should be used and then the information
then converted with suitable tools.
axel.