for MSD calculations, you need to pass three ensemble steps.

do following steps (this is not detailed):

1. Draw your polymer's repeating unit and optimize its geometry and minimize its energy using a fast module, i recommend "Forcite". you should use the same setting for both energy and geometry optimization steps.

2. Using "Built" menu, find "repeat unit" and create repeat unit so that Material Studio can identify it from now on.

3. use "built" menu and "Homopolymer" submenu to create 10 chain long polymer of your repeating unit.

4. in order to use amorphous cell module, you need to assign first the charges to your polymer. this is needed as this module uses these charges for calculations.

5. in amorphous cell module, set a density (

so ... what if you copy optimised geometry to new document and start from there? or do you want to restart the averages as well? maybe if you stop pressing Enter in MStudio and use proper MD software such as Gromacs or CP2K life will be easier.

for MSD calculations, you need to pass three ensemble steps.

do following steps (this is not detailed):

1. Draw your polymer's repeating unit and optimize its geometry and minimize its energy using a fast module, i recommend "Forcite". you should use the same setting for both energy and geometry optimization steps.

2. Using "Built" menu, find "repeat unit" and create repeat unit so that Material Studio can identify it from now on.

3. use "built" menu and "Homopolymer" submenu to create 10 chain long polymer of your repeating unit.

4. in order to use amorphous cell module, you need to assign first the charges to your polymer. this is needed as this module uses these charges for calculations.

5. in amorphous cell module, set a density (

Thanks Milad, I think the main problem is the .xsd file, thank you very much on the steps.

Thanks a lot M. A. Khansary  for the usefull explanations

I want to know how one can create amorphous structure of TiO2 using material studio

Thanks