[gmx-users] CNT Deformation after Energy Minimization

[Aishwarya Smriti]

Hi!

I am trying to to do a MD simulation to check interaction of protein with
CNT. After combining the two topologies (made individually), I proceeded on
to Energy Minimization step. The CNT was completely deformed and the
protein out of its place after the run. Attached below are the photos for
reference. What could be causing this? Please help.
Link:
https://drive.google.com/drive/folders/1Dy-Y88Dle_EZUo00SKkk1etcPOixM9U8?usp=sharing
Thanks in advance.

Regards,
Aishwarya Smriti
Senior Undergraduate
Department of Chemical Engineering
Indian Institute of Technology Delhi