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On 26/09/2011 9:04 PM, raj wrote:
<blockquote
cite="mid:CAE-dxS_dGS--Z3JnMxPwanropNTvgmC9Vp6Q6c21_RzMAv6FQA@mail.gmail.com"
type="cite">
<div dir="ltr">Hello,<br>
<br>
I have done simulations on cyclic peptide nanotubes and trying
to calculate the atomic concentration in the x and y axis, to
measure the diameter of the tube. I have tried using the g_rdf,
but the results are confusing to interpret. Here is the steps
which I followed, <br>
<br>
1. using trjconv, rotational and translational motions are
removed from the centered trajectory. <br>
2. and then, g_rdf -f trj.xtc -s ref.gro -n index.ndx -o
out.xvg (I understood that the "-rdf atom" option is the
default one and this will calculate the <span style="font-size:
12pt; line-height: 115%; font-family: "Times New
Roman","serif";">atomic distribution in the x
and y plane) <br>
</span></div>
</blockquote>
<br>
You need to indicate that you want the 2D analysis with a specific
option. Check out g_rdf -h<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAE-dxS_dGS--Z3JnMxPwanropNTvgmC9Vp6Q6c21_RzMAv6FQA@mail.gmail.com"
type="cite">
<div dir="ltr"><span
style="font-size:12.0pt;line-height:115%;font-family:"Times
New Roman","serif"">
<br>
I am not sure whether the elimination of translational and
rotational motions is enough to calculate this property,
should I have to align the structure in the z axis using the
PCA analysis? <br>
<br>
Regards,<br>
Raj.<br>
<br>
</span></div>
<br>
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