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</o:shapelayout></xml><![endif]--></head><body lang=ZH-TW link=blue vlink=purple style='text-justify-trim:punctuation'><div class=WordSection1><p class=MsoNormal><span lang=EN-US>Hi Gromacs users,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I am using GROMACS (ver4.5.3) to run molecular dynamics (MD) simulation. However during my simulation runs, I encountered some problems as stated below:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>1. In NPT condition, the box size undergoes changes, especially at high temperature simulations. However, during semisotropic pressure coupling, the box size changed dramatically at x/y or z direction. That made the box thin and long or flat. On the top of that, it caused fatal error in the runs and the simulations stopped running altogether. Can this situation be prevented ? If so, how can it be done?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>2. I have found that command “g_helix” can calculate helix properties. Nevertheless, my concern is with beta sheet. I did not find any tools in Gromacs that can calculate the ratio of beta sheet from MD trajectories. Do you have any recommendations?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I'd appreciate any help you can give me on this and am looking forward to hearing from you soon.<o:p></o:p></span></p></div></body></html>