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...

    https://nanohub.org/answers/question/2489

  2. Different use of pair style parameters

    Closed | Responses: 1

    Hi 

    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...

    https://nanohub.org/answers/question/2452

  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?

    https://nanohub.org/answers/question/2393

  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...

    https://nanohub.org/answers/question/2392

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

    Closed | Responses: 1

    https://nanohub.org/answers/question/2390

  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...

    https://nanohub.org/answers/question/2374

  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...

    https://nanohub.org/answers/question/2304

  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...

    https://nanohub.org/answers/question/2278

  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...

    https://nanohub.org/answers/question/2198

  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...

    https://nanohub.org/answers/question/2137

  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...

    https://nanohub.org/answers/question/2124

  12. Vladimir Escobar-Barrios

    https://nanohub.org/members/212609

  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...

    https://nanohub.org/answers/question/2082

  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...

    https://nanohub.org/answers/question/2072

  15. Monomers with >4 backbone atoms

    Open | Responses: 2

    Hello,

    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...

    https://nanohub.org/answers/question/2067

  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...

    https://nanohub.org/answers/question/2062

  17. Nylon as a pre-built monomer ?

    Closed | Responses: 1

    Hi,

    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...

    https://nanohub.org/answers/question/2030

  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...

    https://nanohub.org/answers/question/2015

  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,

    Maxime

    https://nanohub.org/answers/question/1979

  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...

    https://nanohub.org/answers/question/1978