<span class="Apple-style-span" style="border-collapse: collapse; ">Hi Mark, sorry, but could you be more specific when</span><div><span class="Apple-style-span" style="border-collapse: collapse; ">you say "Combine the topologies"?</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse; ">Was not it what I had done early? </span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">Thank you </span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">eef</span></div>
<div><br></div><div><span class="Apple-style-span" style="border-collapse: collapse; ">> The error you report is potentially of the everyday<br>> <a href="http://wiki.gromacs.org/index.php/blowing_up" target="_blank" style="color: rgb(0, 0, 204); ">http://wiki.gromacs.org/index.php/blowing_up</a> variety. See<br>
> <a href="http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off" target="_blank" style="color: rgb(0, 0, 204); ">http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off</a><br>
> <br>> First, get your separated-molecules topology and initial structure<br>> working for basic MD. Then combine the topologies. Only then introduce<br>> your next layer of complexity with constraints-restraints. Then worry</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse; ">> about PMF stuff. Even for experts, troubleshooting where something went<br>> wrong is easier if you only make one lot of changes at a time before<br>
> testing for correctness.<br></span>_______________________________________<br>Eudes Eterno Fileti<br>Centro de Ciências Naturais e Humanas<br>Universidade Federal do ABC<br>Rua Santa Adélia, 166 - Bloco B, Sala 1048<br>
09210-170 Santo André - SP Brasil<br>+55.11.4437-8408<br>skype: eefileti<br><a href="http://cromo.ufabc.edu.br/~fileti/">http://cromo.ufabc.edu.br/~fileti/</a><br>
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