[lammps-users] Question about how to setup an NPT run...

I’m sorry I have to ask such a basis question. I’m sure I’ll feel more foolish later. I guess I need a LAMMPS for Dummys" book that explains how to run it rather explaining commands. As a taxpayer I can say this is one result of government funding I am proud of!!! It’s architecture is amazing and I look forward to building and running it on GPUs soon.

I want to run simple 3D simulations of a polymer (31 atoms ) with the COMPASS force field in LAMMPS using NPT at 300 Kelvins for 900 time steps
of 1.0e-15 second step duration. NanoEngineer-1 allows me to do this and I can watch the molecule vibrating. I’m hoping to show that LAMMPS gives
similar results to show that my LAMMPS input file is reasonably correct. I have built xmovie under CYGWIN and can watch the results of the dump files
generated by LAMMPS - including the sample dump for xmovie. I get some good results, e,g, atoms changing position, using the minimize command - the geometry does change. However my use of fix nve, nvt, npt all result in no atom movement.

My runs currently result in the same atom coordinates for every time step. I know my use of the fix command has got be be bogus.
I am fairly certain my geometry file is good since I modified msi2lmp to read my molecular machine part file generated by NanoEngineer-1.
I modified NanoEngineer-1 so I can type atoms as I draw a molecule as NanoEngineer-1 is an open source molecular CAD package. I hope to
post my changes to the two software applications. I almost have a self-avoiding walk (SAW) software completed that will use a molecule template file
from NanoEngineer-1 to populate a MD cell in a random fashion. I can currently specify templates for several molecules and define their relationships so a polymer is built from “mers” and water and other molecules can be randomly placed in the MD cell. I still have to add the cross-linking.

The software does collision detection to prevent collisions between molecule chains, rings, etc. Eventually, I want to call LAMMPS from inside the SAW to relax the system. I also want the software to cross-link polymer chains based on some user specified distance from the positions on the polymer where the cross-linker should attach to. Call LAMMPS after placing an atom in the MD cell will allow more frequent opportunities to cross-link since the geometry will have changed. I’m hoping this will be a “poor-mans” Amorphous Cell software. If any of this effort is successful it will be released on source forge as open source.

I have modified NanoEngineer-1 to use COMPASS (published values only) and I will eventually work to add other force fields and atom models to NanoEngineer-1.

Thanks in advance,



you forgot the most important thing: a copy of your input.
it is difficult to give advice without.

to know how to use LAMMPS, you should study the
inputs in the examples directory.
to know how to run an MD, you need to learn how it
works from an MD text book.