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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link="#0563C1" vlink="#954F72"><div class=WordSection1><p class=MsoPlainText>Dear GMX-Users,<o:p></o:p></p><p class=MsoPlainText> <o:p></o:p></p><p class=MsoPlainText>I am running some simulations of unsolvated DNA base pair dimers, with a topology generated from a structure previously optimised with quantum mechanical models. Because these structures have been highly-optimised it is important that Gromacs begins the MD with these atom positions.<o:p></o:p></p><p class=MsoPlainText> <o:p></o:p></p><p class=MsoPlainText>After generating the topology with pdb2gmx I get the structure file (gc.gro) with the configuration seen below (after_pdb2gmx.jpg):<o:p></o:p></p><p class=MsoPlainText> <o:p></o:p></p><p class=MsoPlainText><img width=448 height=476 style='width:4.6666in;height:4.9583in' id="Picture_x0020_4" src="cid:image001.jpg@01D61E2B.0E61DD50" alt="A close up of a logo Description automatically generated"><o:p></o:p></p><p class=MsoPlainText> <o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt'>This configuration matches the optimised input structure. However, when I examine the trajectory (.trr) produced by running my NVT simulation (the MDP file for which is attached), the first timestep is very different from the input gc.gro structure, as seen below (first_nvt_frame.jpg):</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt'><img width=448 height=474 style='width:4.6666in;height:4.9375in' id="Picture_x0020_5" src="cid:image002.jpg@01D61E2B.0E61DD50" alt="A close up of a logo Description automatically generated"></span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt'>The discrepancy is largest with the hydrogen atoms (which are not constrained of course), but all the atoms have been slightly shifted from the input configuration. Please could someone fill me in on the source of these position changes, and how I can modify my methods to avoid these.</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt'>Thank you and b</span><span lang=EN-US style='font-size:11.0pt;mso-fareast-language:EN-GB'>est regards,</span><o:p></o:p></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;mso-fareast-language:EN-GB'> </span><o:p></o:p></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;mso-fareast-language:EN-GB'>Max Winokan</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;mso-fareast-language:EN-GB'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;mso-fareast-language:EN-GB'>PhD Candidate in Theoretical Physics</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;mso-fareast-language:EN-GB'>Leverhulme Quantum Biology Doctoral Training Centre University of Surrey</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;mso-fareast-language:EN-GB'>GU2 7XH Guildford</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;mso-fareast-language:EN-GB'>United Kingdom</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;mso-fareast-language:EN-GB'>Office: 03AZ04</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt'>Email: <a href="mailto:m.winokan@surrey.ac.uk"><span style='color:#0563C1'>m.winokan@surrey.ac.uk</span></a></span><o:p></o:p></p><p class=MsoPlainText> <o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt'><o:p> </o:p></span></p></div></body></html>