Eudes Fileti wrote:
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.
> Hi Mark, sorry, but could you be more specific when
> you say "Combine the topologies"?
> Was not it what I had done early?
Indeed, you had done something very close to a successful combination,
and I did not see a problem with it. However your subsequent
observations could have been caused by all manner of problems, including
a bad initial structure. Such a structure would be easier to identify if
you can trust your topology. In your case, initially using a topology
with two copies of the same [molecule] will be a good point from which
to start.
For example
[ moleculetype ]
Benzene 3
[ atoms ]
C1
C2
C3
C4
C5
C6
[ bonds ]
etc.
...
[ system ]
Two benzenes
[ molecules ]
Benzene 2
Mark
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