[gmx-users] g_dist with multiple chains of molecules
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 14 22:46:38 CEST 2011
Sanku M wrote:
> 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.
You can split the group within make_ndx. There are various splitting keywords
(like 'splitat' or 'splitres') that can divide up your index groups. Then
script the 100 calls to g_dist.
> 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.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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