Tags: tool:polymod

All Categories (1-20 of 38)

  1. Atom coordinates in Lammps data file are incorrect

    Closed | Responses: 0

    Dear Developers,

    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...

    http://nanohub.org/answers/question/2072

  2. Monomers with >4 backbone atoms

    Open | Responses: 2

    Hello,

    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...

    http://nanohub.org/answers/question/2067

  3. 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...

    http://nanohub.org/answers/question/2062

  4. Nylon as a pre-built monomer ?

    Closed | Responses: 1

    Hi,

    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...

    http://nanohub.org/answers/question/2030

  5. How to input the initial monomer file for creating the condensation polymer if I have the xyz file of the monomer molecule?

    Closed | Responses: 1

    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...

    http://nanohub.org/answers/question/2015

  6. Building polymer around an molecule

    Closed | Responses: 1

    Just have a quick question, is there any possibility to build a polymer around an molecule such as a graphene flake?

    Many thanks,

    Maxime

    http://nanohub.org/answers/question/1979

  7. Total energy in Dreiding

    Closed | Responses: 1

    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.

    The epsilon...

    http://nanohub.org/answers/question/1978

  8. Differentiating multiple chains

    Closed | Responses: 1

    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...

    http://nanohub.org/answers/question/1950

  9. Pair style selection

    Closed | Responses: 1

    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...

    http://nanohub.org/answers/question/1946

  10. How do I add two different monomers to the tool and specify each on its own?

    Closed | Responses: 1

    http://nanohub.org/answers/question/1940

  11. PEEK, PGMA modeling

    Closed | Responses: 1

    Is it possible to create PEEK and Poly(glycidyl methacrylate) molecular structure in this tool?

    Can that structure be output to run MD?

    http://nanohub.org/answers/question/1935

  12. Is it possible to create polymers which contains Silicon?

    Closed | Responses: 1

    I'm trying to model PDMS, which contains Silicon atoms. The result of the simulation is an error: "Unknown element Si". Any suggestion?

    http://nanohub.org/answers/question/1920

  13. Stress Strain Curve Question

    Closed | Responses: 2

    Hello,

    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...

    http://nanohub.org/answers/question/1887

  14. How to obtain stress-strain curve

    Closed | Responses: 2

    Hello,

    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.

    Thanks,

    Paul

    http://nanohub.org/answers/question/1884

  15. Use the generated initial configuration in a larger simulation box

    Closed | Responses: 0

    Dear all,

    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...

    http://nanohub.org/answers/question/1845

  16. How to change density of polymer to more than 1.0 g/cm3

    Closed | Responses: 0

    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/cm.

    I thought ,...

    http://nanohub.org/answers/question/1833

  17. Local version?

    Closed | Responses: 0

    Is it possible to use Polymer Modeler locally on my computer?

     

     

    http://nanohub.org/answers/question/1829

  18. What are the Dreiding paramters for graphene ?

    Closed | Responses: 1

    Hi,

    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...

    http://nanohub.org/answers/question/1596

  19. 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.

    Closed | Responses: 1

    http://nanohub.org/answers/question/1589

  20. how to get a final pdb structure

    Closed | Responses: 1

    http://nanohub.org/answers/question/1563