[gmx-users] g_dist with multiple chains of molecules

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jul 15 04:59:01 CEST 2011

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.


> 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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110715/4fce875b/attachment.html>

More information about the gromacs.org_gmx-users mailing list