[gmx-users] Distance calculation

[Justin Lemkul]

On 11/27/18 12:37 PM, rose rahmani wrote:
> Great! Non-hydrogen is generally for all AAs, but i want non-hydrogen atoms
> of each AA number 1, 2, 3 to be representative of one adsorption. Moreover,
> if 4 non-hydrogen atoms of AA were in <0.5 nm, this should be considered as
> one adsorption not 4!  How should i come up with these challenges?

Your criteria need to be based on either (1) a minimum distance of any 
atom that satisfies a cutoff or (2) the COM of a group of atoms.

You can easily create index groups for any residue, side chain, etc. 
that you want to consider.

> And as i'm not much skilled in programming, is there any useful examples
> for implementing python or perl in GROMACS?

You don't implement Python or Perl in GROMACS. These are programming 
languages of their own. I suggest them because they are very easy to use 
for parsing text files, which is precisely what GROMACS gives you.

Learn to code. It's an essential skill in this field.

-Justin

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Justin A. Lemkul, Ph.D.
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