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About missing bond angle error
Closed | Responses: 1
Hi, I keep getting error 'Bond angle for atom 5 is NaN'. I am trying to run my monomer's pdb file using polymer modeler. The pdb file appears to be fine to me when I visuial, so...
https://nanohub.org/answers/question/2489
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Different use of pair style parameters
Closed | Responses: 1
Hi
Why does the pair style change in MD and minimization steps. Pair style and pair coeff. parameters. I'm trying to simulate PE and I notice that the pair style changes...
https://nanohub.org/answers/question/2452
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How to upload lammps data file from previous run?
Closed | Responses: 15
I am trying to upload a previous data file but can't copy paste the data. is there any other ways?
https://nanohub.org/answers/question/2393
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Issue in building large polymer system
Closed | Responses: 1
Is it normal to see: "submitting polymer model to remote site ..." for more than 3 hrs for a large number of chains and monomers (100 chains and 1000 monomer). The simulation is still...
https://nanohub.org/answers/question/2392
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How do i make build oriented /crystalline polymers conforming along the same direction using polymer modeler in nanohub.org
Closed | Responses: 1
https://nanohub.org/answers/question/2390
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Problem Modeling Polycarbonate
Closed | Responses: 1
Hi I'm trying to model polycarbonate and am having problems once using the MD steps. I've tried using the below Z-matrix but the ring structure doesn't survive the simulation. I then...
https://nanohub.org/answers/question/2374
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Is silicon still supported?
Closed | Responses: 1
While attempting to run simulations of PDMS with Polymer Modeler, the error message "Unknown element: Si" is displayed. Version 3.33 shows that Si is supported. Is it still supported...
https://nanohub.org/answers/question/2304
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2D periodic structure builder ?
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
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Error in generating PLA polymer structure
Closed | Responses: 1
I'm trying to built a very simple PLA chain composed by only 3 monomers of lactic acid (LAC).
I'm new with the tool, anyway I understood after some attempts how to generate the...
https://nanohub.org/answers/question/2198
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Changing termination of the poly
Closed | Responses: 0
Hi all,
I am trying to use this software to build Poly(dimethyloxilate), however I want the termination to be CH3 instead of H. Henceforth I am trying to write my z matrices like below...
https://nanohub.org/answers/question/2137
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No Temperature Change
Closed | Responses: 0
When trying to follow the Glass Transition Temperature guide in the supporting documents, after I run the simulation I get a set of data points with 0.0 K held constant across all 50,000 data...
https://nanohub.org/answers/question/2124
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Vladimir Escobar-Barrios
https://nanohub.org/members/212609
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Atom number limits in monomer
Closed | Responses: 2
Dear "Polymer Modeler" Developers,
Is there any limit that restricts the length of backbone chain and the length of side-chain in a monomer?
I am trying to build...
https://nanohub.org/answers/question/2082
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Atom coordinates in Lammps data file are incorrect
Open | Responses: 1
Dear Developers,
The coordinates of atoms in the Lammps data file produced by the simulation choice "Lammps input files only" are not correct. It seems to be the wrapped...
https://nanohub.org/answers/question/2072
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Monomers with >4 backbone atoms
Open | Responses: 2
Hello,
I am trying to build poly(ethylene glycol). I've stated the number of backbone atoms as 5 in my z-matrix, but after running the build simulation, it shows my backbone...
https://nanohub.org/answers/question/2067
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What does this error mean?
Closed | Responses: 1
Hello! I am getting this error.. what does this mean?
"Expected a real on line 4 of file monomer.xyz, but found "C".
I am trying to make a...
https://nanohub.org/answers/question/2062
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Nylon as a pre-built monomer ?
Closed | Responses: 1
Hi,
I found the Polymer Modeler tool on nano hub today, and the First Time User Guide seems to suggest that it includes Nylon as a pre-built monomer. Yet in the online version I cannot...
https://nanohub.org/answers/question/2030
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How to input the initial monomer file for creating the condensation polymer if I have the xyz file of the monomer molecule?
Closed | Responses: 2
I have the xyz file for a monomer (Lactic Acid)
I want to create the polymer Poly Lactic Acid (condensation polymer) using the xyz file for monomer.
I tries running the same...
https://nanohub.org/answers/question/2015
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Building polymer around an molecule
Closed | Responses: 1
Just have a quick question, is there any possibility to build a polymer around an molecule such as a graphene flake?
Many thanks,
Maxime
https://nanohub.org/answers/question/1979
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Total energy in Dreiding
Closed | Responses: 1
I have tested a simple example using Polymer Modeler.
I found that in the lammps input generated by this module, the minimization parts are divided into 3 steps.
The epsilon...
https://nanohub.org/answers/question/1978