[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:
> 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.

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.
> Sanku


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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