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Atom coordinates in Lammps data file are incorrect
Closed | Responses: 0
The coordinates of atoms in the Lammps data file produced by the simulation choice "Lammps input files only" are not correct. It seems to be the wrapped...
Monomers with >4 backbone atoms
Open | Responses: 2
I am trying to build poly(ethylene glycol). I've stated the number of backbone atoms as 5 in my z-matrix, but after running the build simulation, it shows my backbone...
What does this error mean?
Closed | Responses: 1
Hello! I am getting this error.. what does this mean?
"Expected a real on line 4 of file monomer.xyz, but found "C".
I am trying to make a...
Nylon as a pre-built monomer ?
I found the Polymer Modeler tool on nano hub today, and the First Time User Guide seems to suggest that it includes Nylon as a pre-built monomer. Yet in the online version I...
How to input the initial monomer file for creating the condensation polymer if I have the xyz file of the monomer molecule?
I have the xyz file for a monomer (Lactic Acid)
I want to create the polymer Poly Lactic Acid (condensation polymer) using the xyz file for monomer.
I tries running the same...
Building polymer around an molecule
Just have a quick question, is there any possibility to build a polymer around an molecule such as a graphene flake?
Total energy in Dreiding
I have tested a simple example using Polymer Modeler.
I found that in the lammps input generated by this module, the minimization parts are divided into 3 steps.
Differentiating multiple chains
Does the final LAMMPS output file fundamentally differentiate atoms of the same chain vs. the atoms in a different chain. i.e. say if I am making a polyethylene, will the carbon-hydrogen...
Pair style selection
I tried to model polyethylene and obtained a lammps data file for it. It has the pair coefficents. However, it does not have a pair style in the lammps data file. I selected dreiding potential...
How do I add two different monomers to the tool and specify each on its own?
PEEK, PGMA modeling
Is it possible to create PEEK and Poly(glycidyl methacrylate) molecular structure in this tool?
Can that structure be output to run MD?
Is it possible to create polymers which contains Silicon?
I'm trying to model PDMS, which contains Silicon atoms. The result of the simulation is an error: "Unknown element Si". Any suggestion?
Stress Strain Curve Question
Closed | Responses: 2
Great tool! I have a few technical questions.
1. What are the units of the output Pressures? (Press, Pxx. Pyy, ...., Pyz)
2. I would like to establish a...
How to obtain stress-strain curve
Is it possible to obtain a stress-strain curve for a polymer with your tool? I would like to measure Young's Modulus of your polymers.
Use the generated initial configuration in a larger simulation box
I have generated successfully an initial configuration of PE in a 50x50x50 A^3 box.
However, once in LAMMPS, I am interested in studying the interaction of...
How to change density of polymer to more than 1.0 g/cm3
Hi , i am using LAMMPS to find out friction of between PMMA and some metal substrates . But i need PMMA which is higher than density of 1.0g/cm3 .
I thought ,...
Is it possible to use Polymer Modeler locally on my computer?
What are the Dreiding paramters for graphene ?
I am using lammps to simulate PMMA-graphene composite system. I used polymer modeller to create the PMMA chains. I want to add the graphene sheet but I am not sure what...
when I runn with my own exe.lammps 3 minimize has done but at fix 1 all nvt temp 300.0 300.0 100.0 this error apear: ERROR: All pair coeffs are not set (../pair.cpp:175) I will be very thankfull.
how to get a final pdb structure