Hi together,
I am a phd student from Germany dealing with Dissipative Particle Dynamics studies.
I need some help using LAMMPS and the COMPASS force field. Looking through the manual and the example scripts is very laborious and I hope someone can provide me a script snippet to get forward.
My task is to calculate some thermodynamic values using the COMPASS force field:
- COMPASS with cutoff Coulomb
- COMPASS with long-range Coulomb
for some small molecules uniformly distributed in a box. For example 10 water molecules interacting with a single methanol molecule. The atom coordinates are available.
Many thanks in advance and every help is appreciated.
Kind regards,
Andreas
Andreas,
I need some help using LAMMPS and the COMPASS force field. Looking through
the manual and the example scripts is very laborious and I hope someone can
provide me a script snippet to get forward.
Being a scientist (or trying to be) is a laborious reality. Why not
considering other career options if "laborious" is not your forte?
My task is to calculate some thermodynamic values using the COMPASS force
field:
- COMPASS with cutoff Coulomb
- COMPASS with long-range Coulomb
If nobody here gets back to you, you may try looking into the Towhee Monte
Carlo code at:
http://towhee.sourceforge.net
Towhee has Compass implemented (version 1) and has the capacity of
outputting input and data
files in Lammps format.
I have not used myself the Compass FF but I have successfully employed
Towhee sometimes this way to produce input files for Lammps on other
systems/FFs.
Carlos
Above all, I would like to make very clear that I am not affraid of work! I hoped that some kind people could help me who are experienced with LAMMPS. I guess it’s common practice… Thank you. Andreas
You can look at the tools/msi2lmp tool which can create
input files suitable for LAMMPS.
Steve
Thanks for your reply. I guess the data input will not be the problem. The read_dumb command allows reading mol files so that will be fine. The problem I have are the parameters (, , , , , , , . ) especially the coefficients for the COMPASS ff. Are they all needed? Which are (very) important? When not set is there a default behaviour? Are the atom types calculated automatically? Because of that I asked for a basic example. But I will investigate on that. Kind regards Andreas
AT > Hi Steve,
AT >
AT > Am 21.06.2013 16:42, schrieb Steve Plimpton:
AT > > You can look at the tools/msi2lmp tool which can create
AT > > input files suitable for LAMMPS.
AT > >
AT > > Steve
AT > Thanks for your reply. I guess the data input will not be the problem.
AT > The read_dumb command allows reading mol files so that will be fine.
coordinates and topology are not the same thing.
AT > The problem I have are the parameters (pair_coeff
AT > <http://lammps.sandia.gov/doc/pair_coeff.html>, bond_coeff
AT > <http://lammps.sandia.gov/doc/bond_coeff.html>, angle_coeff
AT > <http://lammps.sandia.gov/doc/angle_coeff.html>, dihedral_coeff
AT > <http://lammps.sandia.gov/doc/dihedral_coeff.html>, improper_coeff
AT > <http://lammps.sandia.gov/doc/improper_coeff.html>, kspace_style
AT > <http://lammps.sandia.gov/doc/kspace_style.html>, dielectric
AT > <http://lammps.sandia.gov/doc/dielectric.html>, special_bonds
AT > <http://lammps.sandia.gov/doc/special_bonds.html>. ) especially the
AT > coefficients for the COMPASS ff.
AT > Are they all needed?
probably.
AT > Which are (very) important?
you bet.
AT > When not set is there a default behaviour?
yes, do nothing.
AT > Are the atom types calculated automatically?
never. this is an input parameter and part of the model you want to simulate. lammps provides a simulation engine, not a model building system. at least not for molecular systems.
AT > Because of that I asked for a basic example. But I will investigate on that.
have you tried searching the lammps mailing list archive? it may come as a surprise to you, but you are not the first person that is asking about COMPASS.
axel.
AT >
AT > Kind regards
AT > Andreas
AT >
AT >
AT >