[gmx-users] Re:Indexing specific atoms

shayamra at post.tau.ac.il shayamra at post.tau.ac.il
Fri Feb 19 11:09:58 CET 2010

Hello Parthiban,

Can you elaborate more on the 'wrong answer'?
Perhaps the following link can shed some light on the 'wrong' answer:
[Deals with g_dist and PBC]


Quoting parthiban at ncbs.res.in:

> Hello,
> Can anyone tell, how to index two specific atoms, (one form protein and
> one from ligand)
> eg; 440th atom of protein & 450th atom of small molecule or OED of small
> molecule.
> My second question is:
> how to calculate the distance b/w these two atoms.
> i tried g_dist by including the indexed file with this, but the graph
> displays a wrong answer.
> thanks
> In advance.
> Parthiban.
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