Tags: tool:polymod

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  1. 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...

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

  2. 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...

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

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

    Closed | Responses: 1

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

  4. 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?

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

  5. 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?

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

  6. 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...

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

  7. How to obtain stress-strain curve

    Closed | Responses: 1

    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

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

  8. 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...

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

  9. 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/cm3 .

    I thought ,...

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

  10. Local version?

    Closed | Responses: 0

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

     

     

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

  11. 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...

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

  12. 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

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

  13. how to get a final pdb structure

    Closed | Responses: 1

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

  14. Why does my simulation end with an error?

    Closed | Responses: 1

    Hi,

    I'm interested in building long polymer chains and was eager to try out this tool. However, it appears that I get an error when I begin a simulation of a polymer built from...

    https://nanohub.org/answers/question/1498

  15. Polymer modeler and Mavericks

    Closed | Responses: 2

    Dear Sir, I'm trying to launch polymer modeler tool in a Mavericks MacOs machine and the site seems to be loading but nothing happens. My java version is updated (version 7 update 60). Can...

    https://nanohub.org/answers/question/1394

  16. Is there a way to specify an orthogonal but non-cubic simulation box or is a cubic box the only option?

    Closed | Responses: 1

    https://nanohub.org/answers/question/1243

  17. I can’t get LAMMPS output files

    Closed | Responses: 1

    I’m trying to run a simulation of Nylon (PA6) using z-matrix. So it works when I try to get structure output only, but in case of LAMMPS output files it makes an error like that: problem...

    https://nanohub.org/answers/question/1230

  18. Builder error

    Closed | Responses: 2

    Hi,

    When I try to construct a single polymer chain either with the available monomers or with my own z-matrix, i get the following output in the log:

    ERROR: builder failed:...

    https://nanohub.org/answers/question/1206

  19. Can i get the simulation for catechol using nanohub?I did it for chitin and cellulose and got results cathechol is not a polymer.

    Closed | Responses: 1

    https://nanohub.org/answers/question/1034

  20. Proper z-matrix format

    Closed | Responses: 1

    Dear Sir

    I am finding it hard to make the z-matrix. I see that the z-matrices of all polymers within the tool starts with H as the initial atom. Open babel can give me the matrix...

    https://nanohub.org/answers/question/1029