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

Justin Lemkul jalemkul at vt.edu
Sun Jan 6 02:31:58 CET 2013

On 1/5/13 8:29 PM, Xu Dong Huang wrote:
> 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)

At minimum, you need to post the contents of your topology and .mdp file. 
Without that information, no one can make any assessment of what's going on. 
Images of the starting and ending configurations can also be useful.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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