Tags: tool:polymod

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  1. 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

  2. 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

  3. how to get a final pdb structure

    Closed | Responses: 1

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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. Building certain polymers

    Closed | Responses: 1

    Hello,

    I am using Polymer Builder for the first time. I am trying to build teo polymers. One of them is called PE-OC6https://nanohub.org/answers/question/1008

  12. error when producing z-matrix

    Open | Responses: 1

    Dear Sir, I tried to build 10 chains of Polyethylene, each contains 10 monomers. I wanted to produce only the z-matrix as the output. But it was failed. The error message I saw at the end was...

    https://nanohub.org/answers/question/911

  13. z-matrix of Polyacrylamide monomer

    Closed | Responses: 2

    Dear The Polymer Modeler developers! I build the z-matrix of Polyacrylamide monomer which is give below. But in process of simulation of structure of polymer I get bad structure. Maybe I was...

    https://nanohub.org/answers/question/895

  14. introduce a solvent

    Closed | Responses: 1

    Diar The Polymer Modeler developers! Can I introduce a solvent such as water or other in the simulation of polymers in Polymer Modeler? Thank you. Alexander

    https://nanohub.org/answers/question/865

  15. missing bonds

    Closed | Responses: 1

    Hi I am trying to generate a polystyrene structure. Initially I was aiming for a single chain with 20 monomers. But once I loaded the lammps data file in vmd, I saw some bonds were missing....

    https://nanohub.org/answers/question/836

  16. error during equalization with polyethylene structure

    Closed | Responses: 2

    Hi,

    I tried to model a polyethylene structure(50 monomers and 15 chains). I used mostly default settings. but while I am running the NVT equailization (I changed the timestep into 1...

    https://nanohub.org/answers/question/781

  17. save input data file

    Open | Responses: 1

    HI, I would like to know whether I can save the polymer chain I made in polymer modeler. Thanks AZadeh

    https://nanohub.org/answers/question/745

  18. limited number of polymer chains

    Open | Responses: 4

    Currently, I tried to build 100 PE chains with 10 monomers each. However, the PolymerModeler keeps...

    https://nanohub.org/answers/question/703

  19. “ERROR: Illegal fix nvt/npt/nph command”

    Open | Responses: 1

    I built a PE chain by using Polymer Modeler. It seems working well, however, the follwing error occurs “ERROR: Illegal fix nvt/npt/nph command” when you run LAMMPS with the input...

    https://nanohub.org/answers/question/686

  20. How can I resolve the connection problem?

    Closed | Responses: 1

    How can I resolved the connection problem? indeed I try to run in my nanoHUB.org the launch tools of polymer modeler but I am not directed to the polymer modeler’s...

    https://nanohub.org/answers/question/660