<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><div>Dear Gromacs users,</div><div>I set up a simulation between the DNA fragment and 6 podophyllotoxin molecules, the topology files were generated with acpype, simulation time</div><div>was 2.8 nanoseconds, but the results are not what I expected. 4 molecules of PTOX formed an aggregate and then formed hydrogen bonds with the end of the DNA molecule. Could this happen because of the topology file?</div><div>Thanks in advance</div><div>Hovakim Grabski</div></div></div></body></html>