DNA simulations are very sensitive to force field, topology and simulation<br>protocols. In order to find out why this aggregation happened, some information<br>is needed, such as how big was the DNA fragment, how were calculated<br>
the long-ranged electrostatic interactions... From your post I assume that<br>acpype was used to generate the polophyllotoxin topology, but not the<br>DNA topology, right? I ask this question because the<br>DNA topology is easily constructed directly with pdb2gmx, <br>
considering that the nucleotides already appear as building blocks <br>in GROMACS. If this was not the case, consider rebuilding the whole<br>system, because I don't know if acpype parameters are reliable to<br>use in DNA molecules. Besides that, 2.8 ns is too short to obtain<br>
anything meaningfull in DNA simulations. <br><br>Best regards<br><br>Paulo A. Netz,<br>Instituto de Química, <br>UFRGS, Porto Alegre, Brazil<br> <br><br><div class="gmail_quote">2012/3/30 Hovakim Grabski <span dir="ltr"><<a href="mailto:hovakim_grabski@yahoo.com">hovakim_grabski@yahoo.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="font-size:12pt;font-family:times new roman,new york,times,serif"><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><span class="HOEnZb"><font color="#888888"><div>Hovakim Grabski</div></font></span></div></div></div><br>--<br>
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