Step 3.  Build a LAMMPS input configuration for the isolated molecule.

In this example, we create a LAMMPS-compliant input configuration for an isolated molecule.  

The source code for the program that accomplishes this task, lammps_input_readpdb.f is included in the source directory.

To compile this code, move to the directory with the *.f file and the makefile and type the command

make make_lammps_input

To execute the code, move the executable, a.out, to the directory with the necessary input files and type the command

a.out

Included in the example directory are 

make_pdb_output_mod.pdb (input, modified pdb format, output from Step 2.)
intra_input.txt (input file)
intra_input_001.txt (output, copy of input file)
lammps_output_001.txt (output, lammps input configuration, needed for step 5)
intra_output_001.txt (output, list of types of modes, needed for step 4)

Included in the source directory:

lammps_input_readpdb.f (main program)
makefile (compilation instructions)






MSE 614
University of Tennessee, Knoxville
David Keffer
dkeffer@utk.edu
February 24, 2016