<div><br></div><div><br></div><div>HI</div><div>What is the math definition of the radii of gyration about the principal axes in Gromacs?</div><div><br></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "> I use the command g_gyrate -p</span></div>
<div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><br> For lysozyme , I got =><br> 0.922754 1.22249 1.25603<br><br> but in some paper, the authors got<br>
=> 0.660 0.833 0.991<br><br> It is a quite difference.</span></div><div><br></div><div>From David => </div><div>"<span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">The difference seems to be a constant factor.</span></div>
<div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">Gromacs computes<br>sqrt (sum m (r-r_com)^2 / sum m)<br>I'm pretty sure it says so in the manual."</span></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">1. so the different factor is <span class="Apple-style-span" style="font-size: 13px; "> sum m , not sum_N, right ? (N= number of atoms)</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: 13px; ">2. the choice of the principal axes of the protein molecule is a standard process ?</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> => I mean <span class="Apple-style-span" style="font-size: 13px; ">the principal axes of the protein molecule is fixed, right ?</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> => I mean the math of <span class="Apple-style-span" style="font-size: 13px; ">the principal axes of the protein molecule is defined all over the world , right ?</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Thank you</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Lin</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>
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<br></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">On 2010-08-14 23.49, Chih-Ying Lin wrote:<br>><br>><br>><br>> Hi<br>> To Calculate the radii of gyration about the principal axes<br>
><br>> I use the command<br>> g_gyrate -p<br>><br>> For lysozyme , I got =><br>> 0.922754 1.22249 1.25603<br>><br>> but in some paper, the authors got<br>> => 0.660 0.833 0.991<br>
><br>> It is a quite difference.<br>><br>> what is the definition of the radii of gyration about the principal axes ?<br>> i have checked the Gromacs manual but see nothing there.<br><br>The difference seems to be a constant factor.<br>
Gromacs computes<br>sqrt (sum m (r-r_com)^2 / sum m)<br>I'm pretty sure it says so in the manual.<br><br><br>><br>><br>> Thank you<br>><br>> Lin<br>><br></span></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>
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