[gmx-users] g_dist with multiple chains of molecules

Sanku M msanku65 at yahoo.com
Thu Jul 14 22:37:50 CEST 2011

  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.

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.

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