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Hello everybody,<br><br>I tried to run a simulated annealing protocol with 500 molecules of perfluorohexane, trying to optimize their structure and keep on with further equilibration.<br>Since in the end of simulated annealing there were a lot of holes in the NPT box, I've now tried to restrain the positions of the perfluorohexane molecules using -DPOSRES (I've attached the mdp file).<br><br>The problem is that mdrun keeps running in background but there's no output showing in the sa.log file. What could be the problem?<br><br>Thank you.<br><br><br> </body>
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