I constructed an amorphous cell with 2 polymer chains and 600 argon molecules in order to prevent ring catenations. Can I somehow delete those molecules step-by-step (e.g. 200 molecules at a time), and optimize each time in order to end with an optimized amorphous cell that only contains my polymer chains?
http://accelrys.com/products/datasheets/amorphous-cell.pdf
http://www.icdd.com/ppxrd/11/presentations/tuesday/simon_bates-amorphous_materials-a_structural_perspective.pdf
Article Molecular modeling of cellulose in amorphous state. Part I: ...
http://pubs.rsc.org/en/content/articlelanding/2002/cc/b110019j/unauth#!divAbstract
Dear Donya,
I was told that I could write a script, but since I don‘t know how to do that I just tried to delete the molecules one by one. But then the I get an error because the trajectory is change. So I did get an answer, but I haven‘t solved my problem yet.
Hi Ulrike,
Thank you for your prompt reply.
I have the same problem. I need to remove H2 gas from my system. If I could get any solution, I'll let you know.
Cheer,
Donya
Hi Donya,
I managed to remove my spacer molecules! The problem ist the .xtd file. So if you copy your cell into a new 3D atomistic document you will have a .xsd file where you can delete the molecules manually. I hope that helps!
I am facing some issue and I am new in simulation. I want to prepare a membrane using PDMS polymer along with certain percentage of ZIF-8 in it. For this I need only some part of ZIF-8 not the entire unit cell and for this I have to select some of the part but when I take out some of it part I am not able optimize its geomatery using compass I face the forcefield error . And if i use universal forcefield then when I make the membrane with pdms polymer the bonds lengths and angles of ZIF-8 changes and it becomes totally disorder. Please help me out if you have understand what problem I am facing. Waiting for your positive response
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