Dear all,
I would like to see the result of each atom’s charge in material studio.
I know there are several tools for change lammps outfile to arc file. like lmp2arc.
But, I would like to see the charge result in material studio.
Is there any way to do that ??
Why you insist on this practice?
Apart from visualizing atomic charges, it’s really useful to write them automatically in pdb files.
Have you any idea?
Why you insist on this practice?
Apart from visualizing atomic charges, it's really useful to write them
automatically in pdb files.
recommending to write out simulation configurations in PDB format file is
bad advice.
the PDB file format is effectively obsolete (since 2013) and has many
deficiencies and limitations (e.g. limited precision of coordinates or
number of atoms per segment). while many programs can read/write this
format, few of those actually implement it correctly or can handle all
correctly formatted files, and not all files with "extensions" (i.e. not
fully correct files) can be read by programs where the pdb reader is
conforming to the documented PDB standard.
there are quite a few visualization/analysis programs, that can read LAMMPS
native dumps (atom style or custom style).
http://lammps.sandia.gov/viz.html
also, LAMMPS has a built in render feature (dump image or dump movie) that
can access all kinds of internal data.
axel.
Very Well
If pdb is not the pretty case, so what format should be used while being general enough to be handled by most software?
Pdb includes atom types, charge and residue.
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Very Well
If pdb is not the pretty case, so what format should be used while being
general enough to be handled by most software?
there is not "the one perfect file format(tm)". many people have tried to
devise such a thing, but it always failed for a number of reasons.
Pdb includes atom types, charge and residue.
nope. the PDB standard defines an atom _name_, which is inferred from the
geometry, but has nothing to do with a force field atom type. including
atom types would be a big problem, because atom typing can be quite
different between different force fields.
as mentioned before, the native LAMMPS (text mode) dump style is much more
flexible and allows to output any kind of per-atom property.
axel.
Dear all,
thanks for your very helpful advises.
But, my question is not solved yet.
What I would like to do is to see the charge distribution on Material studio.
If I make output file of atom’s position and charge, how could I convert that file to use in material studio ?
Dear all,
thanks for your very helpful advises.
But, my question is not solved yet.
What I would like to do is to see the charge distribution on Material
studio.
If I make output file of atom's position and charge, how could I convert
that file to use in material studio ?
please note, that this is really a question about materials studio and
not about LAMMPS and thus - strictly speaking - off-topic for this mailing
list.
i suggest you ask in a user support forum for materials studio instead.
axel.
Dear Albert,
I made system which has two graphene electrode and some solvent.
The charge of graphene was allowed to fluctuate by using fix qeq.
and, I would like to see the distribution of graphene charge on material studio. but, I don’t know how to make arc or pdb file to use is material studio.