[gmx-users] Distance calculation

Justin Lemkul jalemkul at vt.edu
Tue Nov 27 18:53:12 CET 2018

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 A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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