Urgent Help with LAMMPS examples

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1

Dear all,

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:
quartz.pdb
or

test_opt.pdb
top_silicates.inp (rtf)

par_silicates.inp (prm)

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

important note:
I don’t want any protein or lipid examples because I found so many but I don’t need them

Many thanks,
Rajab

par_silicates.prm (5.35 KB)

quartz_init.pdb (4.02 KB)

test_opt.pdb (121 KB)

top_silicates.rtf (10.9 KB)

2

Dear all,

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.

you are being awfully vague and confusing here. who is "everyone" and
what is "my contribution" or "my system"?

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,

what you are asking for is something very specific and somewhat
complex unless you have significant experience with MD and using force
fields yourself. thus it is highly unlikely that you can just learn
what you need to learn from looking at a couple of examples or blindly
running some scripts. it is usually easy to silence warnings and
produce a working input deck, but that says nothing about the accuracy
and transferability of the resulting topology.

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.

using ch2lmp is a not a good strategy unless you are an expert with
CHARMM parameterization and the corresponding input file formats.
dealing with those is fairly straightforward for simple biopolymers,
but anything out of the ordinary (non-canonical amino acids, ligand
molecules, hetero groups, transition metals and so on) requires
detailed knowledge and some experience that has to be acquired over a
longer period (say a few months to a couple of years or more). getting
things right can be quite challenging for unusual compounds.

For examples, Im using the files located in ch2lmp examples (toppar/
silicates/)
when I run VMD to get PSF file using the files below:
quartz.pdb
or
test_opt.pdb
top_silicates.inp (rtf)
par_silicates.inp (prm)

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

obviously ch2lmp cannot recognize the residue that you have. most
likely due to files that don't follow the expected conventions for
CHARMM force fields. it is usually simpler to build a topology
directly using some script to suitable tool and make it output a
suitable data file directly (see the LAMMPS docs). going through the
step of using a converter just adds another possible point of failure
to your procedure.

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

what you are asking for is a "complete package", i.e. that somebody
else is going to do the work that is essentially yours and provide the
expertise that you don't have. for that you will likely have to offer
more than a "please help me". in other words, what you are asking for
is more like a collaboration than a favor.

important note:
I don't want any protein or lipid examples because I found so many but I
don't need them

well, but they *do* show the principle of how to build a data file just as well.

axel