On 15/07/2011 6:37 AM, Sanku M wrote:
Hi,
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.
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.
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.
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.
Mark
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.
I looked at the mailing list but I could not find any solutions for
these. Any help will be appreciated.
Sanku
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