Questions & Answers (1-20 of 56)

1. 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...

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

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

   Q&A|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

3. Builder error

   Q&A|Open | 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

4. Building certain polymers

   Q&A|Open | 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

5. Can i get the simulation for catechol using nanohub?I did it for chitin and cellulose and got results cathechol is not a polymer.

   Q&A|Open | Responses: 1

   https://nanohub.org/answers/question/1034

6. cross-link

   Q&A|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...

   https://nanohub.org/answers/question/650

7. error during equalization with polyethylene structure

   Q&A|Open | 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

8. error when producing z-matrix

   Q&A|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

9. How can I resolve the connection problem?

   Q&A|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 workspace.

   Please...

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

10. how to get a final pdb structure

    Q&A|Open | Responses: 1

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

11. I can’t get LAMMPS output files

    Q&A|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

12. introduce a solvent

    Q&A|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

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

    Q&A|Open | Responses: 1

    https://nanohub.org/answers/question/1243

14. limited number of polymer chains

    Q&A|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

15. missing bonds

    Q&A|Open | 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. To...

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

16. Polymer modeler and Mavericks

    Q&A|Open | 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

17. Proper z-matrix format

    Q&A|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

18. save input data file

    Q&A|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

19. What are the Dreiding paramters for graphene ?

    Q&A|Open | 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 bond_coeff,...

    https://nanohub.org/answers/question/1596

20. 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.

    Q&A|Closed | Responses: 1

    https://nanohub.org/answers/question/1589