[gmx-users] question

[Andrew Bostick]

Dear Justin,

My previous problem was solved after I used all-bonds instead of hbonds in
constraint section of mdp file. (I got the topology for my ligand using
antechamber).

After completion of NVT equilibration phase, I viewed nvt.gro using vmd.

Please see the related figure in the following link:

https://www.dropbox.com/s/i3ezsacp5jxotin/figure.png?dl=0

What is the reason of this problem and how to resolve that?

Any help will highly appreciated.