[gmx-users] after NVT run, molecule becomes dispersed/ loose

[Xu Dong Huang]

Dear users,

I have a defined polymer .gro file and I ran energy minimization on it. However, when I attempt to run NVT on the polymer in a vacuum (box, no solvent), and I view the output .gro and trajectory in VMD, I see that my polymer is no longer a star, the beads are flying in every random direction, no beads are in bond connection as they should be. Any insight into why my polymer blew up in vacuum? (please let me know what kind of additional information you'd like to see)

Thanks,

Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudongh at eden.rutgers.edu