hello dear
i have simulated water in lammps.data file has been built in vmd and output file consists( .xyz and .data).to view and show atoms in cubic (of course to show walls )output i want to work with packmol software.has anybody worked with packmol to send link of download of software and tutorial of it?is my work resoanable?
i appreaciate anyhelp.
thankyou very much
Only time for a very quick reply.
http://www.ime.unicamp.br/~martinez/packmol/examples/
PACKMOL creates coordinate files (either in XYZ or PDB format). These
files only contain only the position of every atom. You will need to
use a molecule builder to add topology information (bonds, angles,
etc...), and force-field parameters, to create the files which LAMMPS
needs to read in order to run a simulation (IE: a DATA file and an
INPUT script). Each tool is quite different, and is optimized to work
with different force-fields. Here is a list of some of those tools
that I know about:
A) Topotools currently automatically generates CHARMm force-field parameters.
B) Moltemplate generates OPLSAA, AMBER/GAFF, TraPPd force-field parameters.
C) EMC generates COMPASS, PCFF, CHARMM, OPLS, and TraPPe force field
parameters), although I have not tried it yet. Pieter gave a good
talk describing it here:
http://lammps.sandia.gov/workshops/Aug13/intVeld/2013.08.07_EMC_Builder.pdf
D) Molecular Dynamics Studio:
http://sourceforge.net/projects/moleculardynami/
You will have to look at the examples (and documentation) which come
with these tools to decide which one you want to use.
Andrew