Dear Gromacs users, I set up a simulation between the DNA fragment and 6 podophyllotoxin molecules, the topology files were generated with acpype, simulation time 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? Thanks in advance Hovakim Grabski
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