[gmx-users] Re: Constraints - PMF - Different Molecules

Eudes Fileti fileti at ufabc.edu.br
Mon Nov 17 13:23:50 CET 2008

Hi Mark, sorry, but could you be more specific whenyou say "Combine the
Was not it what I had done early?
Thank you

> The error you report is potentially of the everyday
> http://wiki.gromacs.org/index.php/blowing_up variety. See
> 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.
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166 - Bloco B, Sala 1048
09210-170  Santo André - SP Brasil
skype: eefileti
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