[gmx-users] How can measure the end-yo end distance of a peptide from the .xtc file

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 23 17:46:48 CEST 2009

haifeng YUAN wrote:
> Dear all,
>         I would like to get the distance information of the small 
> peptide chain from the .xtc file, but the g_mindist seems can only get 
> the distance information from one group to another. How I can get the 
> end to end distance? I mean  the distance between an end atom  of the 
> short chain to the other end atom?

g_dist with appropriate index groups.


>         Thanks in advance.
> Cheers,
> Haifeng YUAN
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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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