Hi All,
I am a new lammps user. Can anyone show me how to generate the data file from a pdb structure file? Is there any existing script that can handle it or convert from other MD program’s input?
Thanks a lot.
Jianping
Hi Jianping,
Have you checked the tools/ch2lmp directory? The charmm2lammps.pl script operates on a pdb file and transforms it into lammps files. Read the documentation there and see if that will do what you need.
Joanne
Hi Jianping,
Have you checked the tools/ch2lmp directory? The charmm2lammps.pl
script operates on a pdb file and transforms it into lammps files.
Read the documentation there and see if that will do what you need.
well, to make this work, you also have to first create
a matching .psf file with either charmm or NAMD/VMD's psfgen.
there are tutorials for both sofware packages around.
the generation of the .psf file is the real work, as it
requires to identify the residues that make the topology
of your molecule and thus determine the various bonded
interactions and force field parameters needed.
for the sake of completeness, one also has to remark, that
this process can become rather non-trivial, if the .pdb
contains non-standard residues or is otherwise "special".
cheers,
axel.
Hi All,
I used the kspace_style pppm 0.0001 command for my md simulation.
I got the error:
brick FFT buffer size/proc = 10648 3375 5808
ERROR: Cannot use FFTs with FFT_NONE set
ERROR on proc 0: Could not create 3d FFT plan.
Can you tell me what is wrong with my simulation? Is it possible that my FFT library was not installed correctly? How to fix it?
Thanks a lot.
Jianping
Your LAMMPS installation was likely compiled without linking to any FFT libraries. You need to recompile LAMMPS with an appropriate FFT flag set. See the documentation on FFT at http://lammps.sandia.gov/doc/Section_start.html#2_3 ( Editing a new low-level Makefile.foo part 5)
Joanne