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On 15/07/2011 6:37 AM, Sanku M wrote:
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<div>Hi,</div>
<div> I am running a simulation where I have 100 chains of
molecule in a box . I am trying to calculate the distance
between two particular atoms ( present in each molecule)
averaged over all the chains of molecule. i.e If I have atom
C1 and C2 in each of the molecule-chain, I want to calculate
the distance between C1 and C2 atom in each chain and average
over them.</div>
<div>I was trying to use gromacs 4.0.7 g_dist tool . For that,
I first created two index-groups of all C1 and C2 . But. I
realized that g_dist will give me actually the distance
between center of mass of all C1 and center of mass of all C2
which is NOT certainly I was looking for.</div>
<div> So, I was wondering whether there is any other tool which
can split the entire index group by deviding it by total
number of chains and then calculate each individual distances
for each chain and then do an average over them.</div>
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<br>
Check out g_dist -h. There are some other tools suggested there that
look at inter-group distances in a different ways, and one of them
works well for you.<br>
<br>
Mark<br>
<br>
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<div>An analogous tool exists for g_gyrate where where one can
use -nmol option to split the entire index accordingly and
calculate the radius of gyration averaged over all the
molecules. I was looking for something for calculating
distances between two atoms for many chain molecules.</div>
<div><br>
</div>
<div>I looked at the mailing list but I could not find any
solutions for these. Any help will be appreciated.</div>
<div><br>
</div>
<div>Sanku</div>
<div> </div>
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