[gmx-users] question

Andrew Bostick andrew.bostick1 at gmail.com
Sun Oct 4 19:57:08 CEST 2015

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

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

Please see the related figure in the following link:


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

Any help will highly appreciated.

More information about the gromacs.org_gmx-users mailing list