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how to get a final pdb structure
Q&A|Open | Responses: 1
https://nanohub.org/answers/question/1563
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Why does my simulation end with an error?
Q&A|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 one...
https://nanohub.org/answers/question/1498
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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
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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
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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
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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
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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
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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
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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
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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
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z-matrix of Polyacrylamide monomer
Q&A|Closed | Responses: 3
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
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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
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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
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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
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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
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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
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“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
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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
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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