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,...
need help with pha polymers
Q&A|Closed | Responses: 1
C -1.20709 0.69200 0.38922
invalid z matrix for polymer
i want to make olegomers of pha consiste of 10 monomers I start with homopolymer but it did not work ?
C 1 r2
Jun 09 2023
Exploring the Nano World: Building Nanoscale Structures with Polymer Modeler
Is it possible to put a molecule in the middle of each polymer chain by using polymer modeler?
Q&A|Closed | Responses: 4
How to make p3ht polymers
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...
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...
About missing bond angle error
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...
Different use of pair style parameters
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...
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?
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...
How do i make build oriented /crystalline polymers conforming along the same direction using polymer modeler in nanohub.org
Problem Modeling Polycarbonate
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...
Is silicon still supported?
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...
2D periodic structure builder ?
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...
Error in generating PLA polymer structure
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...
Changing termination of the poly
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...
No Temperature Change
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...
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...