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Custom head / tail numbers
Q&A|Closed | Responses: 0
This tool is brilliant, but it has a significant drawback - when exporting files into .pdb format, it puts the first atom of monomer n+1 into monomer n. When the input is set to z-matrix,...
https://nanohub.org/answers/question/2721
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need help with pha polymers
Q&A|Closed | Responses: 0
15
Energy: -25.8732045
C -1.20709 0.69200 0.38922
C ...
https://nanohub.org/answers/question/2689
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invalid z matrix for polymer
Q&A|Closed | Responses: 1
hello
i want to make olegomers of pha consiste of 10 monomers I start with homopolymer but it did not work ?
0 1
C
C 1 r2
C...
https://nanohub.org/answers/question/2688
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Jun 09 2023
Exploring the Nano World: Building Nanoscale Structures with Polymer Modeler
Exploring the Nano World: Building Nanoscale Structures with Polymer ModelerPresenter:Dr. Tongtong (Tanya) Shen, AppleDate and Time:June 9, 2023; 2:00 - 3:00 PM EDTRegister hereAbstract:The...
https://nanohub.org/events/details/2263
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Is it possible to put a molecule in the middle of each polymer chain by using polymer modeler?
Q&A|Closed | Responses: 5
https://nanohub.org/answers/question/2640
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How to make p3ht polymers
Q&A|Closed | Responses: 5
I want to make a polymer of p3ht but it doesn't work. when I try to make a polymer by uploading a p3ht monomer in z-matrix format, only Monomer-zmatrices,OutputLog,Download is displayed in...
https://nanohub.org/answers/question/2594
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error to create polymer
Q&A|Closed | Responses: 5
I have uploaded a PDB file of PEO with 12 monomers and want to simulate it but its showing unknown element H13.HOW can I resolve this issue. I want to generate this CH3O(CH2CH2O)nCH3...
https://nanohub.org/answers/question/2547
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About missing bond angle error
Q&A|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
Q&A|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?
Q&A|Closed | Responses: 19
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
Q&A|Closed | Responses: 2
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
Q&A|Closed | Responses: 1
https://nanohub.org/answers/question/2390
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Problem Modeling Polycarbonate
Q&A|Closed | Responses: 2
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?
Q&A|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 ?
Q&A|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
Q&A|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
Q&A|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
Q&A|Closed | Responses: 1
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
Q&A|Closed | Responses: 3
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