Tags: tool:polymod

All Categories (1-20 of 51)

  1. About missing bond angle error

    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...


  2. Different use of pair style parameters

    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...


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

    Closed | Responses: 15

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


  4. Issue in building large polymer system

    Closed | Responses: 1

    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...


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

    Closed | Responses: 1


  6. Problem Modeling Polycarbonate

    Closed | Responses: 1

    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...


  7. Is silicon still supported?

    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...


  8. 2D periodic structure builder ?

    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...


  9. Error in generating PLA polymer structure

    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...


  10. Changing termination of the poly

    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...


  11. No Temperature Change

    Closed | Responses: 0

    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...


  12. Vladimir Escobar-Barrios


  13. Atom number limits in monomer

    Closed | Responses: 2

    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...


  14. Atom coordinates in Lammps data file are incorrect

    Open | Responses: 1

    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...


  15. Monomers with >4 backbone atoms

    Open | Responses: 2


    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...


  16. 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...


  17. Nylon as a pre-built monomer ?

    Closed | Responses: 1


    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 cannot...


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

    Closed | Responses: 2

    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...


  19. 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,



  20. 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...