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“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...
Closed | Responses: 2
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:...
Building certain polymers
Closed | Responses: 1
I am using Polymer Builder for the first time. I am trying to build teo polymers. One of them is called PE-OC6http://nanohub.org/answers/question/1008
Can i get the simulation for catechol using nanohub?I did it for chitin and cellulose and got results cathechol is not a polymer.
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...
error during equalization with polyethylene structure
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...
error when producing z-matrix
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...
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...
how to get a final pdb structure
I can’t get LAMMPS output files
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:
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?
Is there a way to specify an orthogonal but non-cubic simulation box or is a cubic box the only option?
limited number of polymer chains
Open | Responses: 4
Currently, I tried to build 100 PE chains with 10 monomers each. However, the PolymerModeler keeps...
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....
Polymer modeler and Mavericks
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...
Proper z-matrix format
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...
save input data file
I would like to know whether I can save the polymer chain I made in polymer modeler.
What are the Dreiding paramters for graphene ?
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...
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.
Why does my simulation end with an error?
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...