<div dir="ltr">How to monitor the motion of center of mass of a protein as it is the case all the time to monitor this during the calculations of diffusion and correlation functions. How far the values will be different if we monitor the motion of backbone atoms rather than the center of mass motion.<br>
<br>I still dont have any idea how to get the diffusion constant using g_velacc. <br><br>Ram. <br><br><div class="gmail_quote">On Sun, Aug 31, 2008 at 4:28 AM, Vitaly Chaban <span dir="ltr"><<a href="mailto:chaban@univer.kharkov.ua">chaban@univer.kharkov.ua</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">> No special reason, just mundane ones: computing the diffusion constant<br>
> through mean square displacement is easier in terms of convergence.<br>
<br>
</div>But it is not applicable in the anisotropic systems, for example in<br>
ones with spatial confinements present... :)<br>
<div class="Ih2E3d"><br>
<br>
<br>
--<br>
Vitaly V. Chaban<br>
School of Chemistry<br>
National University of Kharkiv<br>
Svoboda sq.,4, Kharkiv 61077, Ukraine<br>
email: <a href="mailto:chaban@univer.kharkov.ua">chaban@univer.kharkov.ua</a><br>
skype: vvchaban<br>
<br>
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