All Categories (1-18 of 18)

1. Why does my simulation end with an error?

   Closed | Responses: 1

   Hi,

   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...

   https://nanohub.org/answers/question/1498

2. 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...

   https://nanohub.org/answers/question/1394

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

   Closed | Responses: 1

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

4. 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...

   https://nanohub.org/answers/question/1230

5. Builder error

   Closed | 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

6. 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

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

7. 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...

   https://nanohub.org/answers/question/1029

8. Building certain polymers

   Closed | 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

9. 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...

   https://nanohub.org/answers/question/911

10. 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...

    https://nanohub.org/answers/question/895

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

    https://nanohub.org/answers/question/865

12. 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....

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

13. error during equalization with polyethylene structure

    Closed | 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

14. 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

    https://nanohub.org/answers/question/745

15. limited number of polymer chains

    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

16. “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...

    https://nanohub.org/answers/question/686

17. 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...

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

18. 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...

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