Tags: tool:polymod

All Categories (1-20 of 58)

  1. Custom head / tail numbers

    Q&A|Closed | Responses: 0

    This tool is brilliant, but it has a significant drawback - when exporting files into .pdb format, it puts the first atom of monomer n+1 into monomer n. When the input is set to z-matrix,...


  2. need help with pha polymers

    Q&A|Closed | Responses: 1

        Energy:     -25.8732045
    C         -1.20709        0.69200        0.38922
    C  ...


  3. invalid z matrix for polymer

    Q&A|Closed | Responses: 1


    i want to make olegomers of pha consiste of 10 monomers I start with homopolymer but it did not work ?

    0  1
    C  1  r2


  4. Jun 09 2023

    Exploring the Nano World: Building Nanoscale Structures with Polymer Modeler

    Exploring the Nano World: Building Nanoscale Structures with Polymer ModelerPresenter:Dr. Tongtong (Tanya) Shen, AppleDate and Time:June 9, 2023; 2:00 - 3:00 PM EDTRegister hereAbstract:The...


  5. Is it possible to put a molecule in the middle of each polymer chain by using polymer modeler?

    Q&A|Closed | Responses: 4


  6. How to make p3ht polymers

    Q&A|Closed | Responses: 4

    I want to make a polymer of p3ht but it doesn't work. when I try to make a polymer by uploading a p3ht monomer in z-matrix format, only Monomer-zmatrices,OutputLog,Download is displayed in...


  7. error to create polymer

    Q&A|Closed | Responses: 5

    I have uploaded a PDB file of PEO with 12 monomers and want to simulate it but its showing unknown element H13.HOW can I resolve this issue. I want to generate this CH3O(CH2CH2O)nCH3...


  8. About missing bond angle error

    Q&A|Closed | Responses: 1

    Hi, I keep getting error 'Bond angle for atom 5 is NaN'. I am trying to run my monomer's pdb file using polymer modeler. The pdb file appears to be fine to me when I visuial, so...


  9. Different use of pair style parameters

    Q&A|Closed | Responses: 1


    Why does the pair style change in MD and minimization steps. Pair style and pair coeff. parameters. I'm trying to simulate PE and I notice that the pair style changes...


  10. How to upload lammps data file from previous run?

    Q&A|Closed | Responses: 19

    I am trying to upload a previous data file but can't copy paste the data. is there any other ways?


  11. Issue in building large polymer system

    Q&A|Closed | Responses: 2

    Is it normal to see: "submitting polymer model to remote site ..." for more than 3 hrs for a large number of chains and monomers (100 chains and 1000 monomer). The simulation is still...


  12. How do i make build oriented /crystalline polymers conforming along the same direction using polymer modeler in nanohub.org

    Q&A|Closed | Responses: 1


  13. Problem Modeling Polycarbonate

    Q&A|Closed | Responses: 2

    Hi I'm trying to model polycarbonate and am having problems once using the MD steps. I've tried using the below Z-matrix but the ring structure doesn't survive the simulation. I then...


  14. Is silicon still supported?

    Q&A|Closed | Responses: 1

    While attempting to run simulations of PDMS with Polymer Modeler, the error message "Unknown element: Si" is displayed. Version 3.33 shows that Si is supported. Is it still supported...


  15. 2D periodic structure builder ?

    Q&A|Closed | Responses: 1

    Dear Developers,

    So far I was able to use the polymer modeler tool to build amorphous structures which are periodic in all 3 dimensions. I would however like to perform simulations in...


  16. Error in generating PLA polymer structure

    Q&A|Closed | Responses: 1

    I'm trying to built a very simple PLA chain composed by only 3 monomers of lactic acid (LAC).
    I'm new with the tool, anyway I understood after some attempts how to generate the...


  17. Changing termination of the poly

    Q&A|Closed | Responses: 0

    Hi all,

    I am trying to use this software to build Poly(dimethyloxilate), however I want the termination to be CH3 instead of H. Henceforth I am trying to write my z matrices like below...


  18. No Temperature Change

    Q&A|Closed | Responses: 1

    When trying to follow the Glass Transition Temperature guide in the supporting documents, after I run the simulation I get a set of data points with 0.0 K held constant across all 50,000 data...


  19. Vladimir Escobar-Barrios


  20. Atom number limits in monomer

    Q&A|Closed | Responses: 3

    Dear "Polymer Modeler" Developers,

    Is there any limit that restricts the length of backbone chain and the length of side-chain in a monomer?
    I am trying to build...