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<p>rr>. How far the values will be different if we monitor the motion of backbone atoms rather than the center of mass motion.</p>
<p><br></p>
<p>If the particle is rigid, no difference. If no, it depends on the concrete particle. In most cases, the difference will not be huge.</p>
<p><br></p>
<p> </p>
<p>rr> I still dont have any idea how to get the diffusion constant using g_velacc. </p>
<p><br></p>
<p>g_velacc -acflen 1001 -nonormalize -mol -n index.ndx</p>
<p>g_analyze -f vac.xvg -integrate</p>
<p><br></p>
<p><br></p>
<p><span class=rvts9>-- </span></p>
<p><span class=rvts9>Vitaly V. Chaban</span></p>
<p><span class=rvts9>School of Chemistry</span></p>
<p><span class=rvts9>National University of Kharkiv</span></p>
<p><span class=rvts9>Svoboda sq.,4, Kharkiv 61077, Ukraine</span></p>
<p><span class=rvts9>email: </span><a class=rvts10 href="mailto:chaban@univer.kharkov.ua">chaban@univer.kharkov.ua</a></p>
<p><span class=rvts9>skype: vvchaban</span></p>
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