[gmx-users] Re: Constraints - PMF - Different Molecules (Mark Abraham)

[Mark Abraham]

Eudes Fileti wrote:
> Hello Mark, thanks for your attention.
> I had already made some attempts setting the two molecules
> in the same block (as suggested in the forum) but I had no success.
> I tried to use restraints and constraints and  but run always fails.

The error you report is potentially of the everyday 
http://wiki.gromacs.org/index.php/blowing_up variety. See 
http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off

First, get your separated-molecules topology and initial structure 
working for basic MD. Then combine the topologies. Only then introduce 
your next layer of complexity with constraints-restraints. Then worry 
about PMF stuff. Even for experts, troubleshooting where something went 
wrong is easier if you only make one lot of changes at a time before 
testing for correctness.

Mark