[gmx-users] Problem about simulation at high temperature and ratio of sencondary stuctures

蕭翔駿 r99524009 at ntu.edu.tw
Mon Nov 14 10:33:25 CET 2011

Hi Gromacs users,


I am using GROMACS (ver4.5.3) to run molecular dynamics (MD) simulation.
However during my simulation runs, I encountered some problems as stated


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?


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?


I'd appreciate any help you can give me on this and am looking forward to
hearing from you soon.

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