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
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