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Tags: tool:polymod

All Categories (1-19 of 19)

  1. “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...


  2. Builder error

    Closed | Responses: 2


    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:...


  3. Building certain polymers

    Closed | Responses: 1


    I am using Polymer Builder for the first time. I am trying to build teo polymers. One of them is called PE-OC6http://nanohub.org/answers/question/1008

  4. 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


  5. cross-link

    Closed | Responses: 1

    Dear colleague,

    I was wondering how to incorporate the cross-linking formation in LAMMPS. If I use the create/bond command, the bond is created but I could not assign the force field; I...


  6. error during equalization with polyethylene structure

    Closed | Responses: 2


    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...


  7. 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...


  8. 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...


  9. how to get a final pdb structure

    Closed | Responses: 1


  10. 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...


  11. 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


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

    Closed | Responses: 1


  13. limited number of polymer chains

    Open | Responses: 4

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


  14. 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....


  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...


  16. 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...


  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


  18. Why does my simulation end with an error?

    Closed | Responses: 1


    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...


  19. 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...


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