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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.
Closed | Responses: 1
Proper z-matrix format
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 arrangement I …
Building certain polymers
Hello, I am using Polymer Builder for the first time. I am trying to build teo polymers. One of them is called PE-OC6ImCl (made up of O, Cl anions, N and the aromatic benzene like hexagons) and …
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 …
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 …
introduce a solvent
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
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 …
error during equalization with polyethylene structure
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 femtosecond) I …
save input data file
HI, I would like to know whether I can save the polymer chain I made in polymer modeler. Thanks AZadeh
limited number of polymer chains
Open | Responses: 4
Currently, I tried to build 100 PE chains with 10 monomers each. However, the PolymerModeler keeps showing "ERROR" when it is runnung LAMMPS. It only works the number of chain is small such as less …
"ERROR: Illegal fix nvt/npt/nph command"
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 scripts from …
How can I resolve the connection problem?
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 could you help …
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 would …
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