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Hi,<br><br>I want to simulate a system of linear molecules like CO2 with periodic boundary conditions. I think this can be done with the<br>virtual sites algorithm. I have started with GROMACS today. Do you have some sample scripts for linear molecules which use<br>the virtual site algorithm which could help me? I have read that I need topology files but I dont know how to generate them for virtual sites. <br><br>Thanks in advance.<br> </body>
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