[gmx-users] Distance calculation

[rose rahmani]

On Tue, Nov 27, 2018 at 9:23 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
>
Sure, i do my best. thank you.

>
> Learn to code. It's an essential skill in this field.
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
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>
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