<div dir="ltr">On Mon, Nov 10, 2008 at 17:42, Seunghyun Chung <span dir="ltr"><<a href="mailto:chungsh@umich.edu">chungsh@umich.edu</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Deal all,<br>
Is there any practical approach to choose the right temperature coupling strength for a simulation? For example, if a system behaves differently with weak coupling and strong coupling, which result I should trust?</blockquote>
<div>In general, the coupling lifetime should not interfere with any fast degrees of motion you might have.<br>For example, for pure water (where hydrogen bond lifetime is in the ps region, and OH vibration is in the fs lifetime), the thermostat coupling might be ~0.5 ps, but for a protein, perhaps a value in the area of 1 ps and above might be more suites.<br>
Plotting the temperature devations and/or averages might direct you to the better value.<br><br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Also, I thought giving a very weak nose-hoover thermostat coupling would be similar to the NVE simulation. However, when I run the simulation, the system behaves very weirdly by constantly accelerating and slowing down. will there be any explanation on this behavior?<br>
</blockquote></div>I agree. But did you start applying the weak coupling before or after the system was already equilibrated?<br><br><br> --Omer.<br></div>