I’m PhD student at the final year and LAMMPS stand between me and finishing my PhD.
my problem is I’m not expert with LAMMPS. LAMMPS is new for me. unfortunately, small part of my project LAMMPS involve in it. I made a new system that include LAMMPS and it is running successfully and give me accurate results but the problem is I tested my system in one example (Methane example) and that is not enough. I need more existing and large examples to apply them to my system to proof my contribution and to make everyone use my system and get benefit from it.
What I need exactly any 3 existing examples in PDB format are ready with their typology and parameters files that run in LAMMPS and give accurate results. these examples must be materials structure with atoms not proteins or lipids. For examples, Aluminium surface or cooper or silicates or aluminium silicates(kaolinite) or any examples like them.I was looking every where I couldn’t find like these examples I’m seeking for. All I found, these materials in PDB format but I couldn’t find their topology and parameters files. I found silicates inside the file ch2lmp that locate inside LAMMPS but give me errors and I’m not expert to solve them.
For examples, Im using the files located in ch2lmp examples (toppar/ silicates/)
when I run VMD to get PSF file using the files below:
then to run ch2lmp to generate the (.in) and (.data) after getting PSF file from PSFgen in VMD. In addition, the files (.in) and (.data) are created but I got this warning shown below. After that, I got error when I run the file (.in) in LAMMPS:
Info: using test_opt_autopsf.pdb instead of test_opt_autopsf.crd
Info: lx not set: will use extremes
Info: ly not set: will use extremes
Info: lz not set: will use extremes
Info: creating PSF index
Info: creating fcc water
Info: changed lx to 54.1905 A
Info: changed ly to 44.3377 A
Info: changed lz to 19.7056 A
Info: converting atoms
Info: adding ions: [NaCl] = 0 mol/l (0 Na+, 0 Cl-)
Info: converting bonds
Warning: bond parameter 1 for [ ] was not found
Info: converting angles
Warning: angle parameter 1 for [ ] was not found
Info: converting dihedrals
Warning: dihedral parameter 1 for [ ] was not found
Info: converting impropers
Info: conversion complete
how do I get rid of these warnings?
(I will attach the file I have with this e-mail)
Finally, Please I would like you dear LAMMPS users to help me to find 3 materials examples as I mentioned in the third paragraph or to solve the examples in the silicates file inside LAMMPS
I don’t want any protein or lipid examples because I found so many but I don’t need them
par_silicates.prm (5.35 KB)
quartz_init.pdb (4.02 KB)
test_opt.pdb (121 KB)
top_silicates.rtf (10.9 KB)